Normally, to condemn something, as atheist activists do in fact condemn religion, is implicitly to demand that it should be illegal. If I say that people should not kill each other, or steal each others' stuff, or that banks should not take excessive risks with their depositors' money, then I'm saying we should take coercive measures, either proactively to prevent the activity or retroactively to punish it. It usually doesn't make any sense to say, "This or that is bad, but if you want to do it, go ahead." At first glance the author is raising a valid objection.
There are, however, exceptions to this interpretation. The most important exception follows from the understanding that the government — the collection of institutions that have a near-monopoly on the use of coercive force — is not just a completely neutral third party. People in government (and those who control the government, be it the ruling class or the majority) have their own personal and institutional interests, some of which they can fulfill only to the detriment of the interests of people in general. In such cases we might condemn some activity but also not want the government to enforce that condemnation, not because the activity itself shouldn't be — in a perfect world — coercively prohibited, but because we cannot determine how the government could do so without also having the power to implement its own interests to the detriment of our own.
The position of anti-religious atheists such as myself, who are also secularists, is that the fundamental human right of freedom of religion, i.e. legal secularism, is just such a "negative" right. The purpose of this right is not to establish and protect a good, but rather to prevent a greater evil. We support legal secularism not because we believe religion is a good that must be protected, but rather because we cannot think of a way for the government to stop people from being religious without also giving them the right to be arbitrarily tyrannical. Support for legal secularism has everything to do with the inherent limitations of government and nothing to do with the positive value of religion.
For this reason, you will often see an apparently "schizophrenic" attitude toward religion, especially minority religions such as Islam in the United States. On the one hand, we see nothing at all good about the religion. Even where the religion or religious leaders espouse some good belief, some moral standard we approve of, it's just as bad or worse to espouse a good belief for bad reasons; indeed what makes a reason bad is not that it leads only to bad beliefs, but because it can justify any belief, good or bad. On the other hand, attempts by the government to coercively prohibit or marginalize religious belief are worse than the religion. If the government can prohibit a religious belief, it gains powers that can be used to suppress dissent and democratic debate. So we will often condemn Islam in one breath and in the next vigorously support the "ground-zero mosque." Even if the Park51 Muslim community center were a public relations mistake, it is a mistake that is its owners to make, not ours to prevent.
We can find an eloquent expression of this meta-principle in John Stuart Mill's On Liberty, regarding freedom of speech. Mill does not argue that freedom of speech exists because every opinion is itself good. He argues, rather, that we must have to subject all ideas to criticism. It is only by public criticism and analysis that we can separate good ideas from bad.
But the peculiar evil of silencing the expression of an opinion is, that it is robbing the human race; posterity as well as the existing generation; those who dissent from the opinion, still more than those who hold it. If the opinion is right, they are deprived of the opportunity of exchanging error for truth: if wrong, they lose, what is almost as great a benefit, the clearer perception and livelier impression of truth, produced by its collision with error.We can also add, according to Hegel and Marx, the idea that the collision of thesis and antithesis can produce a new synthesis; whenever we suppress the antithesis to the thesis of common belief, we lose the opportunity to generate a synthesis, new knowledge and new belief.
The case for freedom of religion is different than the case for freedom of speech. What is similar, however, is the idea that a universal right can operate on a meta-level. Just as Mill makes clear that we need freedom of speech not because every opinion is good at the literal, "concrete" level and should be encouraged and promoted, but rather because we must protect the abstract meta-level of open discourse. In much the same sense, anti-religious atheists support secularism not because any religion is good at the literal level, but because the suppression of religion is bad at the abstract meta-level. I can criticize and condemn at the literal level some racist, Nazi screed, call it not only mistaken or false but also despicable and contemptible, yet not compromise in the least the abstract principle of free speech. Indeed the principle of free speech exists so I can condemn speech I consider abhorrent. In just the same sense, I can condemn at the literal level any religion, even the idea of religion without compromising in the least the abstract principle of freedom of religion.
We can therefore conclude that criticism of or antagonism towards religion at the concrete level does not compromise the abstract principle of freedom of religion. The only available counter-argument is that the freedom of religion is not an abstract principle; it operates, rather, at the literal level. For example, the right to personal property operates at the literal level, the ownership of personal property is itself good, and must be protected for its own sake. One could argue, therefore, that anti-religious atheists really are compromising an important human right, because being religious is itself good. But that's a different argument. Construed as an abstract principle, freedom of religion exists as much to facilitate criticism and outright antagonism as well as the practice and belief of religion.
Abstract principles often create apparent contradictions. For example, freedom of speech affords the opportunity to criticize freedom of speech itself, to call for government or social censorship. On the one hand, because freedom of speech is nearly absolute such speech is definitely protected. On the other hand, such speech seems to violate the "spirit" of the principle. It is — if not logically contradictory — at least hypocritical to demand universal free-speech protection to call for the compromise of freedom of speech. We have an intuition that implicitly or explicitly attacking the abstract principle itself is illegitimate in a sense different from the negative qualities of bad ideas in general. It is one thing to claim, "Your idea is wrong, mistaken, odious, or abhorrent;" it seems quite another thing to demand, "Because this idea is wrong, you should not speak it." The first is only an exercise of free speech; the second an attack on not just the speech but the principle of free speech itself. Both statements are technically protected; but we can criticize the second in a way we cannot criticize the first. In the first case if we believe the criticism is correct, we have nothing to say about it. In the second case, we might agree with the underlying criticism (we might agree that the idea really is wrong) yet still criticize the speech: we should not demand that anyone remain silent. Right or wrong, put your idea out there so the world can criticize it.
The StateReligionVIC post might be similarly illegitimate. If we see freedom of religion in the abstract sense, it is illegitimate to demand anti-religious forego our own abstract freedom of "religion", i.e. the freedom to argue that religions are harmful. Again it is important to distinguish criticism of our position from the claim that merely stating our position by itself compromises a human right. Just criticizing our position — just saying that we were somehow mistaken in our estimation of religion, or that the author disagrees with our position — would be entirely legitimate. But the StateReligionVIC article seems to say that just the activity of being "antagonistic" to religion by itself compromises an important human right. To make this criticism stick, the article would have to argue the direct claim that freedom of religion exists because religion itself is good.
But the article itself does not even make that claim, much less argue it. The article argues for the value of religious tolerance, not the value of religion: the article states that atheist and anti-religious blogger P. Z. Myers "seems very oblivious to central role that religious tolerance plays in a pluralist society," arguing for the value of religious tolerance, not religion itself. The article also observes that it's difficult to determine precisely what constitutes "religion."
[W]ithin the realm of human rights, it is extremely difficult to determine [what] the proper scope of the freedoms of conscience, of belief, and of religion are and to identify those freedoms in a general and versatile manner for all citizens.I agree! Thus the principle must be seen in the abstract: we protect freedom of religion regardless of religions' merits, because governments cannot even identify, much less consistently evaluate, religious belief. But these problems are benign regarding private criticism, without the coercive power of "public policy or law." If private criticism misidentifies some behavior, it is simply mistaken, not directly harmful in the same sense that mis-identification or vagueness is directly harmful in public policy and law.
The article makes other arguments, but none of them state, imply or argue the critical minor premise that religion itself is good. For example, the article views advocacy for a society free from religion "as a personal opinion, that can not and should not be advocated as public policy or law." The article does not, however, actually cite any instances where this personal opinion actually is advocated as a public policy or law. It chides some commenters for an unsupported opinion, that "calling the people at ACCESS Ministry 'awful people' was not as useful as saying something specific about what they were doing wrong and why it was wrong." Even if absolutely correct, this criticism fails to go to the initial claim. The author objects to his or her treatment by atheist and anti-religious blogger P. Z. Myers and commenters on his site. But again, even if it were correct, this criticism fails to address the claim. Nothing in the article argues for a literal interpretation of "freedom of religion" over an abstract interpretation.
Not only does the article fail to argue for a literal interpretation, it explicitly calls for anti-religious atheists to censor themselves.
In the course of my comments on the school religion issues, I pointed out that I thought PZ Myers would be useful to point out how ICCOREIS statements about evolution exposed their anti science bias, and that the St. James crew didn't want to confront them on this ... so this was an example of how PZ could be "useful" ...The demand that someone else should say something is just as censorious, compromises freedom just as deeply, as the demand that we should not say something. It is the author himself who is at least demanding we compromising our own human rights, the fundamental right to engage in the discussion of religion according to our own agenda, not any Christian's, Muslim's, or Buddhist's or any accommodationist's agenda.
On the issue of religion in schools I find myself continually begging people who are against the current situation, to use language that makes more sense to people who are not anti religious...
Anti-religious atheists engage in analysis and criticism. We do not, on the whole, advocate anti-religion as a matter of public policy or law, or advocate coercive measures. With the exception of Sam Harris, who states, "Some propositions are so dangerous that it may even be ethical to kill people for believing them,"* a position that has received considerable criticism**, anti-religious atheists confine ourselves to substantive criticism and condemnation of religion itself, its content; we refrain on principle from advocating coercive measures to eliminate religion. We are in exactly the same position regarding freedom of religion as anyone who condemns The Protocols of the Elders of Zion or Mein Kampf as not merely false but also odious and abhorrent. It would be one thing if accommodationists such as the author of the StateReligionVIC article were to criticize or condemn our position or arguments for being false, mistaken or inherently odious; to argue in effect that freedom of religion literally and directly protects religion as itself good. But it is hypocritical to demand that we refrain from criticizing religion because criticism is itself "intolerant", because it violates the abstract principle that religion not be subject to coercion. The first would, I would argue, be simply mistaken; the second demand is itself odious and abhorrent, a violation of the very principle it seeks to uphold.
*The End of Faith, pp. 52-53
**See e.g. Tom Flynn, 2005. "Glimpses of Nirvana." Free Inquiry, volume 25 number 2