Since maybe like the Middle Ages there's been different clothes for boys than for girls, and probably before that. This cannot be denied. Girls (a lot of girls, anyway) like to wear ruffles and sparkles and lace. Boys (most boys, anyway) don't. That's why it's so funny when boys wear girls' clothes.
Think about it. It's all throughout history. Look at movies and TV. The tough-guy male lead wearing a dress and looking awkward or indignant always gets a laugh. Whole plots, even, whole bases for movies' classification in the genre of comedy have hinged on the age-old, fool-proof gag of the male cross dressser.
For evidence I refer to Some Like it Hot, I Was a Male War Bride, Bosom Buddies, Tootsie, the more recent Sorority Boys. What is perhaps an addition to the comedic quality of these examples is that the characters in these films are not drag queens. They are truly trying to disguise themselves, to pass as women. Of course we, the genius audience, can clearly see that they most definitely are not women. But the other characters in the films seem not to see anything out of the ordinary about six-feet-tall, broad shouldered women with Adam's apples and five'o'clock shadows. Maybe that's where some of the comedy comes from: our secret, almost smug knowledge that these characters are completely ignorant of. But it's still really funny to see a guy in a dress.
Yet a girl dressed as a boy somehow doesn't have the same effect. There have been a few movies that feature female cross-dressers, but these are from a slightly different mold as those of the male cross-dressing variety. Boys Don't Cry is not a comedy. There is, of course, the recent example of She's the Man. Most of the comedy in this movie, though, arises not from the girl trying to look like a boy, but rather act like a boy.
Seeing a girl dressed as a boy is somehow not as funny as a boy dressed as a girl. Maybe it's because Shakespeare used it so much. He ruins everything. Of course, in his time, it would have been a boy dressed a girl dressed as a boy, which looks the same as a boy dressed as a boy, which isn't funny at all, unless the boy is funny looking.