Darn, you beat me. I've been meaning to post something about being a female geek for a while now :) Anyway, here's my thoughts on the matter...
I haven't noticed any particular discrepancy between the number of females interested in Unix and females interested in Windows. I think that there tend to be more rabid Linux/*BSD fans than their are rabid windows fans, which may make it difficult to see the real numbers.
I myself feel that video games, which are one of the primary draws of young boys to computers, are targeted almost exclusively at the male population.
Let's take this a step further. How many people do you know that say that they would use Linux, but they need Windows for games? If females are less into games, they have less tying them to Windows, and therefor more freedom to switch.
I disagree that the targetting of games at males drives females away from computers, though. By that reasoning, my brother should be the geek, not me. As children, he used the computer the most, and he's always been heavily into games. I played Oregon Trail and stuff like that from time to time, but in general, I explored instead. I remember sepending hours playing with mathematical programs I didn't understand, and learning to program BASIC on the Apple IIe from this "Computer Programming for Kids" book my mom picked up. I suspect that this is why I ended up in the IT field, and my brother is simply a competent computer user who likes gaming.
Actually, to some extent it may be true. Perhaps the targetting of games at males drives the females who would end up being "marginal geeks" (for lack of a better term) to other activities instead, leaving only those who have little use for computers at all, and the hardcore geeks who are more likely to use alternative OSes.
Another possibility, based on my experience, is that females often have to try harder to prove that they have the least idea about what's going on. This may lead to using Linux/whatever (herein referred to as Linux) as a form of self defense - going a step further in order to be taken seriously. Conversely, it may be that unless a female geek who isn't using Linux is overlooked.
One other thing that I've seen observed by several people (including myself) is that females tend to be interested in more things than males. Females have a bunch of activities, while males tend to focus more on one thing. Big generalization here, and I'm sure it doesn't apply to everyone, but since I'm not the only one who's noticed, I'll mention it anyways :) This may lead to the false assumption that a female is not a geek because she's involved in all these other activities as well. Again, in this case, using Linux simply emphasises that the female is indeed a geek, a fact that might be overlooked otherwise.
I don't perceive using free software as an act of rebellion. Perhaps some females do. I personally use it because I like how Unix works, it does what I need, it's stable, I can mess with the insides in a way that I can't with Windows, and it's free, so I don't have to pirate or pay licensing fees. I also don't perceive being a geek as an act of rebellion (Though other people do, apparently. I've had people assume I'm a feminist simply because I happen to work with computers). Its simply something that I am. If this means that I'm different from how society expects me to be, then that's their problem, not mine. Ok, so perhaps that's a slightly rebellious attitude :) But the point is that I'm not a geek in order to rebel, but that I'm considered a rebel because I'm a geek. Effect, rather than cause.