It's really just because of the stereotypical "Grrl Gamer" figure, who doesn't know much about games but plays them for attention from guys, or the woman who uses her sexuality rather than actual competence to get a job or to market a game. The fact of the matter is there are women like that - and there have been high profile cases of game developers using attractive women to try to sell their game. Note Jessica Chobot's inclusion in Mass Effect 3, for example. Or the case of Jade Raymond, where there's no reason to suspect that she's not totally competent at her job - but when the first Assassin's Creed was released, she was a producer, one of several and not the lead or executive producer. There's no discernible reason that she was made the face of the game besides her appearance.
And there's cases of misogyny essentially being "baited" as with Jennifer Hepler's comment that critics of her writing were simply "Jealous" that she had "an industry job and a vagina". That's hardly the usual situation, but I fear that high profile cases like that can both make misogyny appear to exist to a greater extent than it truly does, and exacerbate the misogyny that legitimately does exist. I also feel that there's a tendency of feminists or people who want to milk feminism for financial gain to take a few of these comments (and let's face it, if there's one thing the internet has taught us, it's that hateful idiots can never entirely be eradicated) and construe them as far more representative than they truly are. And to some extent, this media attention adds to the discrimination, since portraying something as common also portrays it as normal, and therefore acceptable.