I should say, written by males without really thinking how them being female should affect them.
For example, with video game action protagonists like Lara Croft (this may be different in the later ones) and Rayne from BR, there really isn't much characterization as far as how they relate to a life of violence. They're sexy, and they kill stuff. Of course, this is par the course for action heroes as well, who aren't fleshed out either, but it doesn't help them.
I can also certainly consider a few protagonists that were written as men that were damn good, like Ripley. You'll notice, though, that this sort of thing is the case in visual medium, but not written fiction.
With anything that really spells out what the character is thinking, you absolutely need to keep the character's sex in mind. The exact same personality traits in a man or a woman will cause them to develop very differently as people, and obviously this is relative to the culture, but no less true today. The audience, and the character's friends, are going to be more forgiving of fearfulness in a female character than a male, and they're going to be more forgiving of aggression (or alcoholism, or whatever) in a male than a female.
Then onto their life plans, and so on and so forth. To take D&D protagonists, a man is extremely likely to have wildly different motivations for going on as an adventurer than a woman. Or to cite the military, its simultaneously the home of the most traditional of men and the least traditional of women.
So I seriously don't think ignoring the character's sex is a good thing in writing fiction. It works in movies way moreso than in the written word, though, because the actress can fill in the essential humanness.