The latest example, thanks to a link from Lawyers, Guns, and Money, involves a post written by Rebecca Watson at Skepchick reacting to a speech given by Ron Lindsay at a conference called Women In Secularism 2.
The idea that talking about privilege as a social reality is somehow oppressive is no different than being told that calling out racism is the real racism, or that pointing out that defending legal discrimination might well be evidence of bigotry is not a personal attack; it's crap, in other words. Guys like Lindsay, while certainly well-intentioned, tend to miss the point that when someone else notes they are speaking from a perspective of social and cultural privilege, it's just that.
What is not at all pretty, however, is the barely-repressed rage one reads in comments at the Skepchick article. That a woman had the audacity to call out a man seems to stir something horrible in some people. The discussion at LGM is far more restrained, and by and large favorable to Rebecca Watson (which is one reason I visit there a lot; even their trolls are fun). At the heart of the discussion, however, is the largely unexamined idea that, being privileged in one way - feeling superior because they are skeptics rather than gullible goofs like us religious types - won't somehow extend to the rest of their lives. Skeptics and atheists will just naturally be better at all these things (remember how the Soviet Union decried the sexism and racism in the United States, all the while being pretty horrible on these matters? I thought not) including how men relate to women. And since it's men telling everyone how much better they are, it must be true.
It is odd that the sexism in these groups comes as some kind of shock. At least some of us in the religious communities, recognize the reality of sexism and struggle with it openly; for some reason, a woman pointing out that the skeptical/atheist community has similar issues is just wrong, as many men are quite willing to explain, with force if necessary.
The fact is these prejudices are inherent, particularly in groups whose membership is preponderantly male. I'd be more surprised if there wasn't widespread misogyny in such groups. The least that can be done, I suppose, is allow women to behave like people without it becoming somehow oppressive to the powers-that-be. It is working out pretty well in some churches; shouldn't these folks strive to do at least as well?