It's important to remember that there's a huge difference between intolerance of religion, and intolerance of religious people. Certainly tolerance of religious people is very important, since people should not be persecuted because of their beliefs, or forced to act against those beliefs, except in extreme cases (for example, if a person believes that god requires him to commit murder, it's entirely reasonable to force that person to act against his beliefs by preventing him from comitting murder.) Both beast and I are very tolerant of religious people, and think that everyone else should be as well. (Beast, tell me if I'm putting words in your mouth, but I'm pretty sure we're essentially in agreement on these issues.)
However, tolerance of religion is in fact problematic, because it causes people to restrain themselves from pointing out how religion and science are contradictory, and how religion is a major source of strife. Beast and I both think that religion should be defeated by reason, but it is important to remember that this is a battle of ideas, and the weapons are rational arguments, which don't hurt anyone, and education (no, I don't mean indoctrination - I mean teaching facts, and teaching an inquisitive and skeptical nature, and allowing people to make up their own minds). A healthy skepticism is always beneficial whenever one is confronted with surprising claims - be it that God exists and performs miracles, or that some people can predict the future by looking at the stars, or that humans evolved from single-celled creatures - and one should always require evidence to back them up. Religion needs to lose its privileged status as being somehow immune from such skepticism, but somehow the idea of "religious tolerance" has become so ingrained that it is anathema to criticize it.
In sum, one should of course be tolerant towards people who believe differently, but that's no reason not to criticize their beliefs if such beliefs are not only false but also damaging.