I mean the playing field isn't equal. Imagine if the majority of characters in FPS games were female. You start up COD and 90% of the NPCs are female, and your character is female, too. Imagine also that in a COD MP game, women dominated the airways. They made sexist comments towards any male player who dared to speak up. The entire culture of COD MP centered around female gamers getting together, having a great time, and occasionally taking verbal pot shots at the minority male players.
In that scenario, you would very likely discover that more women played COD (a FPS game that emphasizes strategy and teamwork over story and character) than men.
Actually I don't want the majority of the characters to be female. I don't believe that is the reason why women don't want to play FPS. Sometimes I play FPS but because they are so linear and I can't affect on the story or the characters I usually don't like them that much. Because in the end FPS is the game where you shoot things and a lot. The gender doesn't mean so much in them than in RPGs.
I have been thinking how much it means to me to play female characters. Would I play more different games if I could play female characters instead of male characters? I think I would still prefer story, characters and romances. I would still prefer a game where I could choose a romance while playing male PC over FPS with a female PC. because there is so many games with male PC it's nice to play female characters for a change but if the situation would be different then I might want to play more male PC.
I believe that many women don't play MP because of the reasons you described. Although I believe many women still will create a male character and still play MP if they want to play it. You could get an impression that more men play MP than females but actually you can't know that for sure. But I think majority of people playing them are men. So only reliable way to know what games female prefer to play is to make study about it.