At the same time, there is nothing inherent in atheism that condones, justifies, or promotes bigotry. We have no "holy" book that can be read (or misread) as advocating bigotry. We have no clergy who are assumed to be a conduit to any sort of divine beings that might make it easier for us to justify bigotry. And even if one recognizes that atheists become atheists by traveling many different paths - not all of which involve reason, critical thinking, skepticism, or freethought - it seems that our lack of "holy" books, clergy, and the like could be relevant. Bigotry might be a bit harder for atheists to justify than it is for at least some religious persons to justify.
And yet, there does seem to be at least one are where atheists are regularly accused of engaging in bigotry against members of one religious group. Interestingly, the accusers often seem to be left-leaning atheists, and the accusations typically involve "Islamophobia."
Consider the following sentiment for a moment:
[Insert name of group here] are immoral and dangerous to society. We should round them all up and get them the hell out of our country before it is too late. They are our enemies and should be treated as such.It seems pretty clear to me that this reflects bigotry and that this remains true regardless of whether we fill in the group with Muslims, Christians, people from Latin America, atheists, or whatever group you prefer. It doesn't seem to matter which group one might select; the result is still bigotry. We're saying that everyone who belongs to this group is evil as a function of their membership in the group, and we're calling for their persecution.
Some atheists seem to have a very difficult time reconciling the importance of criticizing Islam and their fear of "Islamophobia." I do not find Islamophobia to be a helpful construct, as it seems designed to silence much needed criticism. On the other hand, I can and do recognize that anti-Muslim bigotry exists and can be a real problem. If one were to fill in the above group with "Muslims," one would see a fairly clear-cut example of anti-Muslim bigotry.
The difference between anti-Muslim bigotry and criticism of Islam strikes me as so obvious that I struggle to express it. I'm not sure how to explain it to those who seem unwilling or uninterested in grasping it. I acknowledge that there can be cases that seem to blur the lines between criticism of Islam and anti-Muslim bigotry; however, they seem few in number compared to the clear-cut differences. Again, the statement above is a clear example of anti-Muslim bigotry that has nothing to do with criticizing Islam. A call for a reform to take place within Islam seem like an equally clear example of criticizing Islam that has nothing to do with anti-Muslim bigotry.
I see no reason why atheists cannot be every bit as critical of Islam as many of us are of Christianity. Wait a second - that's not entirely true. I do see one reason. Perhaps atheists, at least atheists living in predominately Christian regions, are far more familiar with Christianity than we are with Islam and this might make us feel more comfortable criticizing Christianity than Islam. I can accept that. But this does not explain why some atheists seem to freak out when ex-Muslims or others more knowledgeable about Islam criticize it.
I'd like to see atheists and other secular persons feel perfectly free to criticize any and every religion, just as they would any other bad ideas. At the same time, I'd like to see atheists and other secular individuals recognize and avoid bigotry against religious persons.
For some great discussion on this subject, check out this video of Sam Harris and Maajid Nawaz at the Harvard Kennedy School. Their new book, Islam and the Future of Tolerance: A Dialogue is on my read-as-soon-as-you-have-time list.