Look. I come down squarely on the side of those who complain that there is indeed sexism among atheists. No, it isn't everyone nor is it always overt nor is it as bad many religions, but it is present. I am male but that does not mean that I am immune from observing the kinds of behaviors that strike me as at best rude and all too often as hostile. Moreover, though I think I can parse the arguments that deny the magnitude of the problem, that does not mean that I agree with them, especially when they are themselves examples of the problem. See above.
Recently, a young woman posted on the Atheism forum at Reddit a picture of herself holding a book by Carl Sagan that she had received from her religious mother for Christmas. This ended up becoming a flash point for the ongoing controversy about the prevalence of sexism among atheists. A controversy I should note that has been boiling to some extent for much of this year.
Some feminist, atheist bloggers have expressed their disappointment in the atheists who posted sexist, demeaning things in response to that young woman's picture. They've cited this as yet another example of the kind of hostility women face that discourages involvement in the atheist community. This has sparked replies defending the community as a whole from the charge of sexism, arguing that the problem is contained in only a few bad apples. And the debate kicked off anew.
What I do not think those who are denying the severity of the sexism problem seem to understand is that whether it is a few bad, but vocal, apples causing the problem or not -- by giving them a pass on their behavior we are as a community giving tacit approval of their unwelcoming stance towards female involvement. This creates a feedback loop that reduces the gender diversity of our community, which in turn emboldens the sexists to think they can continue to get away with being hostile, which makes our community seem hostile to women even if the majority of us aren't, which keeps gender diversity low, and so on.
I happen to think that overt and hidden sexism are both an impediment to our community. I think that women have valuable contributions to make, not the least in a chance to promote self reflection regarding sexism and male privilege in ourselves and in our communities. Some of those who refuse to examine potential sexism or refuse see it in themselves are pushing back against women, but they do not represent my views on this matter. I would be happy to see that as active, female participation grows in our community that the sexists get pushed further to the margins as unwelcome social pariahs.
There is some karmic justice in that, given how they insist on treating women now. But as more and more young women like Lunam on Reddit get involved, our community will change, for the better in my opinion. So my advice to the old guard with misogynist tendencies is to be aware that the demographics are shifting. Things are going to be different than what you've grown accustomed to and you are going to have to adapt to remain relevant.
[edit: As was pointed out by my perceptive wife, my use of "young women" could be construed as sexist in itself. I do mean women in general ought to be made more welcome, not just young women. Though what inspired this post was the treatment by atheists of a young (fifteen year old) woman and my last paragraph was meant to be read as though addressed to her and other young people.]