Tolerance as an absolute virtue is trivially self-contradictory: To espouse tolerance as an absolute virtue, one has to be intolerant of intolerance, a blatant contradiction. (I'm always amused when various conservative Christian writers condemn out of one side of their mouths liberal tolerance for just this reason, and demand out of the other side tolerance for their irrational beliefs.)
Arrogance and humility are much too vague to even be discussed as vice and virtue. Is it arrogant to argue that one's position is actually true?
Which leaves us with "civility".
I have, for instance, been accused of making a personal attack (and punished by removal of my blog from his blogroll, an action which cost me literally ones of readers) by a professional philosopher for calling his arguments "usual[ly] intellectually lazy" in the context of a specific post that did not even bother to offer any sort of argument at all for an insulting and false-to-fact conclusion. (The Deacon has deleted the contents of his blog, so his original post is no longer available.)
This seems like a very mild criticism, and a criticism of the man only insofar as his character is reflected in the low quality of his work—on which I had offered a considerable amount of substantive criticism, now deleted with the rest of his blog.
If this relatively mild criticism is seen as incivility, what about admittedly more extreme and relatively uncontroversial incivility? We put murderers, rapists and thieves in prison and call them, well, murderers, rapists and thieves. A considerable number of people—including some conservatives—call President Bush and members of his administration monsters and evil men and women for torture, arbitrary imprisonment, and lying to the American people to justify a naked war of aggression (to name only the most egregious of their offenses). Even those who unconditionally support the President and approve of his actions have offered decidedly uncivil comments about the terrorist criminals responsible for 9/11 and the millions of ordinary Muslims who cheered their crime (again only a sample of their offenses)—uncivil comments with which I myself unreservedly agree. If civility were an absolute virtue, such incivility would be obviously wrong.
Of course, finding that tolerance and civility are not absolute virtues does not entail that they are not virtues at all. They are, rather, virtues relative to the subject under discussion, and justified by their pragmatic effectiveness at actually affecting public discourse and public behavior. Incivility and intolerance has the effect of polarizing debate. In some cases, polarization—such as the polarization between liberal and conservative political views—is not helpful. In other cases polarization—such as the polarization between lawfulness and criminality—the polarization is both effective and warranted by most people's ethical beliefs.
In some cases, the polarization already exists; it seems the case that civility can maintain an unpolarized state, but it does not seem to be able to reverse a state of polarization. The only cure for polarization outside of open warfare seems to be the intellectual humiliation of one side of in the debate. (A notable example is the humiliation of Joseph McCarthy.)
PJ of Christian Feminist criticizes atheist hubris and bemoans a particular atheist reviewer's "mean-spiritedness". (I will ignore that calling someone mean-spirited seems itself somewhat uncivil.) It is definitely the case that the reviewer in question hardly bends over backwards to respect the beliefs of theists. There's no question that the reviewer is uncivil; the question becomes: Is his incivility warranted?
I say it is. The explicitly political agenda of most atheists is very simple: Upholding the establishment clause of the First Amendment, which has been in place for more than two centuries—more than ten generations. And we are still fighting blatant violations of this fundamental Constitutional principle: "under God", "In God we trust", using public funds to promote specific religions and transparent attempts to mask religious proselytization as pseudo-scientific "intelligent design". Madelyn Murray O'Hair was called "the most hated woman in America" for her successful efforts to remove state-mandated religious prayer from public schools. Even PJ herself says,
I think both sides should leave each other alone.Well no shit, Sherlock.
(Of course, this might be easier if most religions, and Christianity in particular, hadn't made such a nasty habit of sticking its nose into places where it has no business, namely politics.)
Why should we believe that civil discourse is going to help now? It's not like the separation of church and state is a new concept that deserves careful consideration of competing points of view. It's a bedrock and well-established Constitutional principle. The establishment clause is the very embodiment of what PJ specifically asks for: That both sides should leave each other alone.
Atheists have, at the political level, honored this request (with the exception, perhaps, of a few cranks who have no status within the atheist community). We do not demand that our public schools teach that there is no God. We do not demand that specifically atheists beliefs be printed on our currency or included in the Pledge of Allegiance. We do not demand that public money be spent in any way to promote our views. To my knowledge, no notable atheist has ever asserted that religious believers were unfit to be citizens. We ask only that the First Amendment be honored as written. For this demand alone we are vilified, hated, insulted, assaulted, our property vandalized and our leaders murdered.
And the Christians accuse us of incivility. The debate has already been polarized. It has been polarized for millennia, and it was not the atheists who originally polarized the discussion. Start actually leaving us alone, and then we can discuss civility. I'm not holding my breath.
 I must remind my readers that the phrase "under God" was specifically inserted into the Pledge to establish the specifically religious character of American democracy vis a vis the "godless communists" of the Soviet Union; an especially ironic move given that the author of the original Pledge, Edward Bellamy, was a dedicated socialist.
 Well, no notable Western atheists. The atrocities of the atheistic Soviet, Chinese and Southeast Asian Communist regimes are universally condemned by atheists in the West on Humanistic grounds.