This started out as a comment to a diary by wiscmass, called "In search of religious tolerance." In this diary, wiscmass was complaining that too many kossacks throw the liberal religious babies out with the fundamentalist bathwater. The comments quickly became a war between liberal religionists and fundamentalist atheists. As someone who belongs to neither group, but who does have my own Neopagan religious beliefs, perhaps I can offer a different way of observing the issues.
(More below the fold.)
It seems to me that religious absolutism, exclusivism, and fundamentalism -- not religion in general -- is what needs examination. Philosophically, when a belief system makes absolute truth claims, it's headed for trouble. When a belief system then declares all other belief systems false and inferior, it's becoming creedist. When the members of a belief system then decide that only the most conservative interpretations of their beliefs are the true ones, and that all other beliefs (including the liberal versions of its own faith) are demonic, it has definitely become creedist.
Combine creedism with a willingness to commit crimes against the Forces of Evil™ and you get crusades and jihads, inquisitions and witch hunts.
Now it is my observation, after 40 years as a polytheologian, that monotheistic belief systems, including western atheism, are the ones most vulnerable to the development of this sequence. Since those belief systems are the ones that have dominated Western culture for 2,000 years, and since they themselves tend to deliberately blur lines of distinction and shades of grey into the more comforting black vs. white worldview of dualism, the moderates and liberals in those belief systems operate in liberal and moderate venues at a disadvantage.
Just as white liberals have to go an extra mile to convince black people that they are not racist, and liberal men to convince liberal women that they aren't sexist, so too must Jewish, Christian, Islamic, and Secular Humanist liberals and moderates go an extra mile to prove to the non-religious and the non-monotheistic that they are not themselves creedist even if many of their co-religionists are.
Is this fair in any absolute ideal of tolerance? No. But it is normal human psychology. When the primary political oppressor in America today has been a political party dominated by violent fundamentalists, now engaged in warfare with other violent fundamentalists, it's easy for us to jump to conclusions when someone starts using religious language.
So as we would say at the beginning of many Neopagan rituals, "Everyone ground and center, take a few deep breaths, now begin."