As a gamer I have been avoiding female protagonists for a while due to how the female body was portrayed and used as a main selling point in most video games, especially in RPGs. Just look at the advertisement banners for some shady browser-based MMOs around the internet. Instant facepalm!
I changed my mind after playing such games as Mirror's Edge and the latest installment of Tomb Raider. These games feature realistic looking, intelligent females. But most importantly, the main focus of these games is to give you a lot of fun as a player.
The problem is not that female or male protagonists are too "sexy". This almost doesn't matter. What matters, however, is that the player sees them as human beings, through their story, struggle, vulnerability, moments of strength, fears, emotions, ... etc.
When a game relies solely on the physique of its protagonist without giving him/her a human background, that's when things fall apart. Players perceive the protagonist as an empty shell and lose any emotional link to him/her, and by extension, to the game itself.