Sexism
We've been talking about sexism in fandom forever. People who complain about the lack of female characters in canon but don't write any of the ones that do exist is a pretty constant topic. We also wonder occasionally if the anti-Mary Sue attitude has made people afraid to write female characters.
I think part of the reason a lot of people are reluctant to write female characters in fanfic is because you get it coming and going. Write her as too strong, she's a Mary Sue or a “man with breasts” (I never have gotten a satisfactory definition of that term). Write her as too flawed and you obviously hate feminism. And of course there's the usual accusations of making her OOC. The stress of getting it wrong in some way is something that's not as present with male characters.