This is actually a topic I have lots to say about. Feminist writing awaits...
First of all, it's important to note that butch =/= masculine and femme =/= feminine.
Secondly, masculinity and femininity are constructed in order to put men on top, and women at the bottom. Femininity, in particular, is enforced in order to make women subservient and pleasing to men, with masculinity being equated with dominance and control. Once you bear that in mind, the portrayal of feminine men and masculine women (or lack thereof) makes a lot of sense.
Feminine men become equated with men that want to please and be subservient to men, which is equated with being gay. Femininity in men is rarely played up positively unless it's clearly intended to be irony or a parody, but most of the time, they are regarded as a throwaway punchline rather than anything else - essentially, masculine men (even ones who aren't heterosexual) want to distance themselves from feminine men as much as they can; boiling them down to laughable stereotypes is the best way to do this.
As for masculine women, Taka is very much correct in saying "butch women challenge male privilege in a way that femme guys don't." By not conforming to femininity, they are, in effect, rejecting the male gaze. And because women are so often defined by their relationships with men, and the actions towards men, and nothing else, butch women are regarded as having little value. Ultimately, the age-old socially-held value that women are only valuable to the extent that they appeal to men still hold strong. That's why they're such a rarity in the media.
However, because masculinity is held up as gender-neutral in society, while femininity never is, a woman can 'get away' with more masculinity than a man can femininity without being labelled 'gender non-conforming'. Few bat an eyelid if, say, women wear jeans and a white T-shirt. But if a man wears even one feminine-coded item of clothing, that is often enough for him to be considered outright 'feminine'.
So in conclusion, basically masculine women have to deal with a lot more ->-bleeped-<- on the whole, but the amount of masculinity that needs to be expressed to be considered 'masculine' is greater.