It would be convenient if we could use objective, secular scientific reasoning to determine the correct moral values. However, the world does not appear to work that way. As I explore in more depth in my series on Meta-Ethical Subjective Relativism, science cannot establish moral laws in the same way it establishes physical laws. A physical law is, by definition, a statement that despite careful and focused and careful effort, we cannot observe any exception. If we do observe an exception to what we thought was a physical law, we do not conclude that a "miracle" happened; we must readjust our construction of physical law to permit the observation. However, the only interesting moral "laws" are those we do observe contraventions of; a moral law prohibiting killing (under specified circumstances) is useful only to the extent that people do actually kill. Since we cannot (or it is not useful to) "falsify" a moral law by observing an exception, we simply cannot apply the scientific method to determine moral law.
There have been other philosophical approaches to determining moral law, but, lacking scientific foundation, all of them suffer from the Universal Philosophical Refutation. Science can "privilege" hypotheses only because the universe itself appears to refuse to contradict the hypothesis, but when the universe does not speak to the conclusions, any premise can, with a little ingenuity, be abandoned or replaced by its opposite without contradiction. There is no objective way you can say, that it is morally wrong to kill a person (under specific circumstances). There is no objective way you can say, we ought to (somehow) maximize the "well-being" of society. There is no objective way you can say that we should do only what everyone always ought to do. I can simply deny it's wrong to kill a person, maximize utility, or be compelled by the categorical imperative, and although we might not like or respect each other, neither of us can find a contradiction in the other's reasoning.
A democracy fundamentally rejects the idea of objective moral law. Instead of "searching for the truth," about morality, we search for ways we can all live together. Some of those ways involve prohibiting or compelling behavior. Democracy is not a simple matter of always doing what the majority says; because we are not completely stupid, we can look at issues at varying levels of abstraction and generality. A majority of us can, for example, strongly disapprove of specific, concrete speech, such as racist or sexist speech, but still strongly approve generally and abstractly of freedom of speech, and we can decide to implement the general and abstract into law. Furthermore, we have learned to institutionalize certain democratic principles, such as the First Amendment, and making the process of changing those principles complicated and difficult. But at the end of the day everything in a democracy is up to the arbitrary preferences, specific and concrete or general and abstract, of the people. The people are sovereign; because the universe constrains only how we can act, not how we ought to act, there is no higher authority on how we ought to act than the preferences of the people.
Because democracy is based on implementing arbitrary preferences, there is no good way to distinguish arbitrary preferences from arbitrary religious preferences. This is precisely the distinction Ebert tries to draw. Religions have not become popular because they completely ignore our natural preferences. Religions forbid murder and theft not because wow! who'd'a thunk it until God said so, but because a religion that excused or required wanton murder and theft would not gain many adherents. Even so, people usually attach all their moral beliefs to God; just as they believe homosexuality is wrong because God says so, they also believe that murder is wrong because God says so. They are mistaken, of course, no God exists to say anything, but they are mistaken about the justification, not the preference. A secularist is simply more direct. As a secularist, I am tolerant of homosexuality simply because I don't have any preference about what people do with their genitals*; I am intolerant of murder because I strongly prefer that people don't go around killing each other (and I don't give a tinker's damn that I'm infringing on the liberty of people who do want to kill others). The difference is not in the kind of preference, only the justification (or lack thereof); because all preferences are arbitrary, it is incoherent to talk about correct or mistaken preferences; preferences are just brute facts. Thus, it does not make sense to distinguish between different kinds of preferences; all preferences have equal standing.
Rather than placing limitations on motives, since motives are essential preferential, the First Amendment places limitations on the purposes and effects of laws. Rather than making the government either supportive or hostile to religion, the establishment and free exercise clauses, the First Amendment makes the government indifferent to religion. Thus, any law that has a primary or exclusive purpose or effect of establishing or suppressing religion is illegitimate. Although it's not consistently applied, the Lemon Test expresses this doctrine. Even if some law might have a "religious" motivation, it is legitimate so long as its primary purpose and effect are secular. Thus, even if the prohibition of murder were religiously motivated, it has a secular purpose and effect of suppressing the killing of human beings. It is sufficient to limit the purpose and effect of laws without addressing their motivations.
I myself am, of course, a strong proponent of absolute reproductive rights of women. However, I think the "religious motivation" argument against laws that would infringe on women's reproductive rights is fundamentally flawed. Laws limiting reproductive rights have a clear secular purpose: laws restricting abortion and contraception aim to and would have the effect of promoting the creation of and protecting human zygotes and blastocysts. Whether these are good secular purposes is a matter of preference (or many preferences, at different levels of generality and abstraction), but they are clearly secular: they address physical, concrete things about which we can have scientific knowledge. The secular/religious distinction does not by itself address reproductive rights.
Ebert does, however, imply a useful moral distinction. Rather than the distinction between religious and secular morality, we can draw a distinction between social and individual morality. Social morality concerns behavior that has a direct effect on others: killing people, hitting them on the head, taking their stuff, polluting their air and water, denying them employment, housing, or economic activity, etc. Even though people might have preferences as strong as they have concerning social morality, individual morality concerns behavior that does not have a direct effect on others: consensual sexual activity*, masturbation, diet, health care choices, assisted suicide/euthanasia of the terminally ill**, and similar activities. Religion, one's preferences about what to believe about God, is perhaps the most obvious form of private morality; as Jefferson says, religion (or lack thereof) "neither picks my pocket nor breaks my leg." By itself, religion has a purely individual effect.I t it tempting, therefore, to locate what are essentially privacy rights in the First Amendment. But that approach ignores most of Supreme Court jurisprudence. Privacy is a right, and therefore any act that affects no one but those who consent is usually considered private. But privacy rights have been located by the Supreme Court, not in the establishment and free exercise clauses of the First Amendment, but in the concept of substantive due process, a consequence of the due process clause of the Fourteenth Amendment.
*that does not have a direct, substantial impact on the transmission of infectious disease.
**with appropriate protection for the poor and mentally ill.
**with appropriate protection for the poor and mentally ill.
The issue over contraception and abortion rights is important, but the argument from the establishment clause is a bad argument. It is impossible in principle and actively contrary to democracy to try to distinguish between certain kinds of arbitrary preferences. Because they involve tangible, material entities and activities, not immaterial, invisible entities such as gods and souls, contraception and abortion are, whether we like it or not, secular matters. The best constitutional arguments, indeed the ones actually made by the Supreme Court in Griswald, Roe and others, are found in substantive due process. We must, in a democracy, let people argue (and vote) for any legitimate law, regardless of their individual motivation. If we do not, then we subvert democracy by making some process sovereign over the will of the people, and, more dangerously, unacceptably privilege those individuals who implement that process.