There is a great blog post from PZ Myers that discusses sexism in atheism. I just want to add that this problem is also found within the skeptical community as well, perhaps not quite to the same extent, but close.
This is just a microcosmic example of what we find in society at large. I would say that the problem of sexism in the atheist and skeptical communities isn’t nearly as entrenched or as vicious as in, say, the gamer, science, or other similar communities, which is a good thing. If we can make the efforts that PZ describes, we can be leaders in including women as equals.
As atheists, skeptics, and secular humanists, we already have a greater sense of, and support for, social justice than the population at large. We need to keep working to include all segments of society in our communities and show the often bigoted, sexist, and racist religious believers what real brotherly, and sisterly, love means.