There have been quite a few high-profile incidents of racism and sexism among some atheist communities recently. These have been followed by the predictable pattern of soul-searching about what can be done to prevent them and get more people who aren't white men involved in atheism, countered by the predictable denial that there's any problem at all by the selectively skeptical.
Now, obviously any community that exists in this society is going to be vulnerable to reproducing this society's ideas of the default person, even if its aims are apparently unrelated to structural discrimination. Privilege is designed to be invisible to its owners, so without a concerted effort to work against it (and even then...), people will inevitably repeat dominant social values even if they don't want to.
But I think these particular atheist communities have more fundamental problems than that.
Firstly, what Tami said in the post linked above:
But there is a difference between seeking to use reason and making skepticism and reason an identity. The latter, I'm beginning to think, results not in injecting more reasonableness into public discourse, but less, as people who are invested in touting their own superior logic are rarely self-aware enough to spot and acknowledge the places where their thinking has been colored by bias. And make no mistake--no one is immune to the biases inherent in our society--not even the guy who calls himself a Skeptic and fancies himself the smartest person in the room.
Secondly, their aims are, by definition incompatible with the ending of kyriarchal systems of privilege.
Their rhetoric makes it very clear that they1 wouldn't be satisfied with a society in which religious belief and lack of religious belief were treated as equal. They want to be above religion, with religious people the subject of disdain for their "irrational" and "obsolete" beliefs.
And there is the problem. They want to be on top of the heap. They dispute the construction of the heap - why are atheists not at the top of it2 - but they don't object to its existence. It's no surprise therefore that debates over "what should the relative position of men and women in the heap be?" are frequent - the alternative answer of destroying the heap entirely is unthinkable.
All forms of oppression are so strongly entangled that it cannot be possible to eliminate one3 without attempting to eliminate all of them. By supporting and encouraging the existence of the heap, they make it impossible to eliminate the other parts of the heap they disagree with.
1 I've had to be fairly non-specific about exactly which atheist communities I'm referring to, because it's not as if there are official denominations of atheist. So the definition is going to have to be somewhat circular: "the sort of atheist I'm talking about is the sort of atheist who fits the description I give". But I hope nevertheless it's obvious enough that there are many atheists and atheist communities that are not like this, and who I'm not talking about here.
2 How far down they are of course varies considerably by country and region, as well as many other factors. Trends suggest that they will get to the top of the heap and be the default eventually, at least in some places, just through weight of numbers.
3 That's not to say that I believe, ad absurdum, that all existing forms of oppression will end simultaneously or not at all. Clearly on some day in the distant future it may be that racism ends but some heterosexism continues, or vice versa. For now, however, all forms are so entangled that trying to end one (or a few) in isolation is doomed to failure.
Given the attempts by some of these atheists to, for instance, redefine religion as mental illness, I think they're more likely to increase the entanglements between oppressions than decrease them.