Yeah, I'm skeptical of the argument she lost because she is a woman. A fair amount of the GOP would have listed Condoleezza Rice and Sarah Palin on their wish list for top of ticket in 2016. Yeah, it isn't proof that misogyny is a myth, but it's hard for me to say that "GOP HATES WOMAN!" when there is clearly a large portion that would vote for a woman that matches their political views.
I still think Hillary lost for the same reason Jeb! lost, namely voters are sick of political dynasties, insiders, and folks that feel entitled to public office. This was a change election and she was the status quo.