I see human emotions such as aggression, territoriality, dominance, mercy, family bonding and group bonding as evolved to improve the chance of an individual or group to pass on its genes. As man evolved reason and language, some of this genetic morality became cultural. Not all social behavior was genetic anymore, some of it had to be taught. Most cultures developed a dual authority, with a chief leading in practical matters while a shaman explained the unexplainable and maintained rules and morality. This in time developed into state and church.
In Western Civilization, the Reformation, Scientific Revolution and Enlightenment challenged to role of the church. Scientists began taking over the role of explaining the unexplainable. Blatantly immoral policies by the medieval Church resulted in multiple alternate systems of understanding God and behaving morally. Religious wars to determine by force of arms which religious system would triumph became unendurable, resulting in the concept of Freedom of Religion. It became accepted that each individual had the right to determine and follow their own preferred system of morality. The Enlightenment produced an alternate system of morality, based in part on Reason, in part on Rights allegedly granted by God.
Me, I'm a devout agnostic. The moral system taught in one's youth is apt to stick. I am able to respect most religious systems. They contain much wisdom of the ages. Many of them (all of them?) are not perfect. They were created in a time of muscle powered weapons, when war was cost effective. They were used and are still used to justify cultural aggression. I still believe in Freedom of Religion, that force or coercion should not be used to expand the scope and territory of an individual's moral system.
But then, the Enlightenment values have been used to justify cultural aggression as well. Many value systems are absolute. They present themselves as superior to all other value systems. Too many value systems tempt followers to use coercion or force to perpetuate themselves. In this case, we have a religious faction attempting to perpetuate religious values, while the ACLU is attempting to perpetuate extensions of Enlightenment values.
Me, I'd as soon see attempts to perpetuate religious values kept out of public schools and government institutions. I wouldn't get hyper about it. If Christians don't mind other religions putting up, say, Samhain decorations on Halloween, or Passover decorations on public property, sure, put up religious Christmas icons as well. As long as it is vaguely mutual.
I see science, reason and government slowly taking over roles once monopolized by religion. Many individuals, however, still hold to religious values as primary and absolute. They will understandably resist the notion that various value systems must be put on an equal footing. I don't anticipate easy answers.
