Intolerance involves a refusal or failure to examine other ideas to look for merits. Atheism is based on principles which naturally give rise to inquiry, investigation, and open-mindedness. Those who claim "atheist intolerance" tend to be advocates of religious ideological protectionism, which they see as threatened by atheist inquiry. They are themselves advocating intolerance when they use the claim of "intolerance" to suppress this inquiry.
Also, although atheists have become increasingly organized in the past few years, atheism is not a centrally-organized entity – 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 in some ways, but that would generally be counter to the principles upon which atheism rests, rather than an indictment of atheism itself.
It is true that atheists are, generally speaking, intolerant of a number of things:
- stupid ideas
- sloppy thinking
- arguments which depend on logical fallacy or rhetorical deception, i.e. are dishonest
- any form of dishonesty
- religion in general, due to the many problems with it:
- really bad ideas being defended solely on the basis of religion
- evil committed in the name of religion
- religious advocacy which claims that morality requires religion
- religious advocates who claim that their religion is the only true source of morality
- religious people who say insane things...
- ...which are taken seriously...
- ...because they are religious
Refusing to tolerate demonstrably bad ideas or the people who promote those ideas is not, however, what is usually meant by intolerance. "Intolerance" is seen as a bad thing because of the refusal to examine and refusal to see the good (throwing out the baby with the bath water); this is a very different thing from considered and specific criticism.