Have you noticed that pretty much all "hardcore" games have male protagonists? These games tell players that they are fantasies for guys to have; women are relegated to the roles of support or prizes in most of these games. It sucks to try to be the hero when the shape of the fantasy is constantly telling you that you're not one.
And then we have the advertising campaigns mentioned in the article that market it explicitly to boys, with girls as a prize.
There have been some big-budget games with character selection screens that let you choose a lady, but how many of them prominently feature that in the marketing? Skyrim, Mass Effect, or Saint's Row all feature a male protagonist on the box, despite me enjoying all of these with a female character.
Hell, even in the realm of little casual games, it's there. I've played a lot of iOS games that have a male character from the start, and offer a female one as something you can unlock... after collecting five zillion coins, or dropping $10 in in-app purchases. Men are normalized, women are an expensive bonus prize.
Trust me, there is a constant message that "video games are for boys" running through much of the medium. Yes, women play them anyway. But we are constantly being told that the big budget action-oriented games are not for us by what roles they offer for us to play.