I'm a lawyer so I do understand that discrimination is a complex issue...
Ouch, I'm beyond my league here.

The writers seem to choose the sex of their characters and they have always regularly chosen more men in every single incarnation of the franchise.
Sure they are more men in Star Trek, that said there are more Men in the Navy (wiki indicates somewhere around 6:1 ratio), and here is an interesting paragraph i managed to dig up:
Gender is the single best predictor of criminal behavior: men commit more crime, and women commit less. This distinction holds throughout history, for all societies, for all groups, and for nearly every crime category. The universality of this fact is really quite remarkable, even though many tend to take it for granted.
http://law.jrank.org/pages/1256/Gender-Crime.html
So Star fleet would presumably have more men than women, and the villains would presumably be more men then females. Hence, more men leading roles than women.