(So much for my blog break. Well, it can start tomorrow. I wrote this long comment over on John Wilkins' Evolving Thoughts blog, and thought it was worth being a post in its own right - here it is with tiny alterations. Please comment, as the theory, when expressed like this, is provisional and could do with some kicking around.)
It does seem that traditional cultures have their "eternal verities" - things that seem to be immutably true about fundamental aspects of the human condition. I put the words "eternal verities" in scare quotes because some of these things may not be verities at all, and certainly not eternal ones. And they won't be identical across all cultures. In modern, pluralistic societies, you'll get different verities believed in by different people - some may still be operating with an "eternal verity" that women are intellectually inferior to men, for example, even though this is neither true nor even a universally-shared illusion. Nonetheless, there are various fundamental "verities" that are likely to be widely accepted even within a pluralistic society. Sometimes, philosophers challenge them directly by arguing that they are not true or well-founded. Sometimes science and technology challenge them less directly. Either way, many people are going to be made very uncomfortable. They execute Socrates, try to deny women the vote, ban human cloning, beat homosexuals, get queasy about interracial marriage, etc.
There may be some deeper explanation as to why the world is like this, but in any event I think it probably is like this.
The theory isn't mine by the way; I borrowed it from Richard Norman. It's Norman's theory of background conditions, or my restatement thereof. I wonder whether it's compatible with Gigerenzer's work, with which I'm unfamiliar. Maybe there's a way of putting Norman's theory on a more rigorous basis.
What role does religion play? I'm not sure that I have the full answer, but I think that a culture's religious beliefs and its pet "eternal verities" will co-evolve. As a result, the religion will be heavily invested in the local set of eternal verities. It will have influenced them and been influenced by them. It tends to preserve them and to resist challenges to them, whether from science or from experimental lifestyles, or wherever else. Religious images of the world will be chock full of these eternal verities, whether it's the eternal verity of human exceptionalism, the eternal verity of free will (in a very strong sense), the eternal verity that women should act in such and such a way in relation to men, the eternal verity that sex is nasty and only redeemed by its procreative potential, the eternal verity that we have only three score years and ten, or whatever it is that the locals believe to be an immutable truth about the world and our condition within it.
Any attack on the local eternal verities, even if not actually intended as an attack on religion, is likely to receive strong counter-attacks from religious sources. Moreover, because religion has picked up a whole lot of these traditional fundamental beliefs that made some sort of sense once but are largely not true, it is always likely to imagine the world in a different way from the way it is imagined by the majority of people who are highly scientifically literate and are keeping up with the developing scientific image of the world. (This para and the immediately preceding one are my addition to the theory.)
If we really want to challenge the eternal verities (as they are imagined to be in our place and time), we can expect opposition from at least some - probably many - religionists. If we are serious, we may feel that we have to counterattack our religious opponents head-on, by pointing out that the religion that gives them their mantle of seeming authority is just not true in the first place.
E.g. to defend the morality of homosexuality, it may not be enough to argue that, by some secular principle, it does no harm. It may not be enough to put pressure on religion to reinterpret its doctrines to accept homosexuality. The best way of getting homosexuality socially accepted, and to stop people defending the local eternal verity that "homosexuality is evil", may be for at least some people to stop talking so much homosexuality itself, and about secular moral theories, or new theology ... and to spend more time promulgating scepticism about religion.
If you really want a transvaluation of values, according to which many things once considered virtues in your society (such as chastity and certain kinds of pietistic humility) are now considered vices, and certain things that were once considered sins are now considered good or at least neutral (e.g. homosexual acts; so-called scientific "hubris"), one of the best things you can do is spread scepticism about religion.
Of course, the fundies and the Vatican are already well aware of this last point, but whereas they call spreading scepticism about religion bad, I call it good.