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This claim is erroneous.
- Intolerance involves a refusal to examine other ideas to look for merits; atheists take great pains (and often display great relish) in examining religion in detail, and frequently observe that religion is not without merit.
- Atheists are not, per se, an organized group, so it doesn't make sense to speak of them as if they were unified in any attitude other than the definitional one, i.e. not believing in God(s). Some individual atheists may be intolerant, but it's not an essential part of being an atheist.