I think that a number of these games aren't really written such that gender makes any difference.
True, CYOAs and interactive fiction in general are unique in that the main character, 'you' can basically just be a cipher that the player mentally fills in with whatever they want, but on the other hand that only works if the story is kept deliberately generic. I'm talking 'find the seven treasures in the giant dungeon and destroy the magical MacGuffin' levels of stuff.
Once you start moving away from the game elements and putting more focus on the story, (which even IF has done over the past fifteen years or so when it went indie) this naturally means plot and character is going to take center stage, which means you really kind of need an actual, specific character. And for a lot of reasons yes, that character usually winds up being male. (Though now I'm a little curious what the statistics are on this particular forum, maybe it does mainly just come down 'most of the writers here are male so most of them are more comfortable writing about guys'.)
Anyway, for what it's worth my contest story will have a female protag. So does the sci-fi story I'm working on for IS. (well...sort of.) The next Big Damn Project on the list is planned to be an ensemble piece, but if that turns out to be as overwhelming as I'm thinking it might it'll probably wind uo mainly being about a woman too, with a few 'intermission' pages stuck here and there from other POVs. (In response to the OP, there's probably a reason most games don't give you a choice--unless the only difference is that you click M or F in the beginning, in which case it's meaningless, writing all those branches for one character can be daunting enough, I can't imagine going through all the trouble to write an 'almost the same but not quite' version to go alongside it, and if for whatever reason it's a completely different plot, then they might as well make a completely different story.