Pharyngula started getting a more feminist slant after the whole "Elevatorgate" incident. One of the few prominent women in the atheist movement made a blog post about how she was at a convention and told a group of people she was going to bed, and one of them followed her into the elevator alone, cornered her, and asked her to come to his room. She made a general statement of, "Guys, don't do that, it's creepy", and she ended up getting a shitstorm of backlash about it. The nature, size, and ferocity of the backlash made PZ aware of the problem of sexism in the atheist movement and he began his crusade of wanting to ensure that atheists held themselves to a higher standard than the patriarchy of religion, so has made it a habit of calling out sexism in the atheist movement when he sees it, as too many are content to sweep it under the rug and simply claim that atheism is more progressive than that.
He's still petulant and overly-confrontational at times, yes, and some of his targets of offense are a bit of a stretch, but I don't have any inherent problem with a person who was suddenly made aware of a gigantic stain on the movement he's at the forefront of and expending a lot of energy trying to make other people see it and help clean it up.