For most of my undergraduate career, I was operating under the assumption that prejudice against women in the professional community was largely a thing of the past. As a result, I felt that quota-based hiring practices, etc. were largely artifacts whose only effect was to diminish male's ability to compete. If nothing else, I thought this was certainly true in science.
Going through graduate school disabused me of this notion, in a variety of ways. Primarily, I was surprised that many female grad students, and virtually every woman over 30, believed women were discriminated against in science. Perception isn't always reality, but it is hard to dismiss someone's opinion without reason, and I didn't have any good reasons. In fact, some pretty good reasons for how this discrimination were happening were explained to me.
Let's take perception. The North American Benthological Society is one of the few society conferences I've attended regularly. The society is small, and seems young, but there are perhaps a few dozen 'stars' of the society. These are the rock stars of the stream ecology world.
As my friend Sally pointed out at the last NABS I attended, the male and female rock stars are very different. The males are out late drinking every night of the conference, going to strip clubs, etc., etc. For many of them it shows in the talks (which tend to be incoherent and rambling; but funny), yet people pack the hall to see them speak because everyone loves them. The comparable women rock stars are generally described with words like scary or intense. The women tend to produce these fantastic (ok...good) talks that don't quite attract the same attention.
Why? Because women in science are judged much harsher than are men! Recent research is now documenting this (see a nice discussion and good references here), and demonstrating that being a woman reduces your odds of getting a paper published in Nature (holy grail for ecologists). In fact, this paper suggested a woman has to be over twice as productive as a man to be viewed with the same esteem.
And this isn't just an abstract factor. This translates into things like funding (pdf), where women are less likely to be getting funding.
So what is causing this? Most male scientists I know are surprised by studies like this. Women scientists are, literally, all over the place in academic science. I think I the male:female ratio of grad students I knew in graduate school was probably skewed slightly towards the female side, and I certainly know a lot of female rock star professors. Overall, I'm guessing it is happening because most scientists don't think its happening.