Wow, good question!
I've also wondered about this, too. I think girls maybe are a bit more interested, during the teenage years at least, in putting themselves in another's shoes. When it comes to reading, at least. So they are more prepared to read about boys, because they are more prepared to... It's probably a reflection on marturity levels. They say that adolescent girls mature sooner than boys. Therefore perhaps they are a bit more tolerant with a main character of the opposition gender.
Also, I think girls' bodies start maturing sooner than boys... and I have a feeling that girls have to put up with a bit more of a difficult time in this regard. I can understand that boys maybe don't want to read about the trials a girl of the same age goes through... they mean nothing to them, at this point in life. This doesn't really apply to historical fiction, so much... I think girls are more interested in emotional journeys and boys more physical - journeys that involve action. They want stuff to happen. They're more hands on, generally. So it's pyschological, and developmental, certainly.
And some of it's historical. Sadly, there's still the reminents (and probably more than that) in our culture of the male-dominance. For centuries, men have looked at themselves as being better. There's a stigma - connations - attached to being "girly", that equal it with being weak. And the society that for centuries perviously has dictatored that men must not cry. So being emotional is being weak as well. I'm sure that some of this still affects young boys/teenage boys today.
We still re-enforce it. The books about strong women in that era - and fantasy - a lot of them (written for that age-group, at least) show women dressing in men's clothing, and engaging in male activities. They have to do this to prove their strength... and if it's something like a boy doing something seen as traditionally a girl's activity, like ballet, his sexuality comes into question, as does his manliness. (I had to study "Billy Elliot" a couple of years ago... and I'm sure that was how some of the guys in my class viewed it).
But I don't think it always applies, either. My brother has read about half the Tamora Pierce books, and most of them are about girls. He loved "The Will of the Empress"... surprisingly. However, I know he struggled having to study a novel about a seventeen year old girl in English because the character and the novel related events that were out of his experience, and had no relevance to him. I know if I'd read a book about a guy that age, when I was my brother's age, chances are I would have had a similar reaction...
