I voted "I don't care."
Not that I'm saying I don't care about the issue or anything, but rather, given a good setup, if you've developed the story right there's no way a well-developed male protagonist is going to make the game any better or worse than a well-developed female protagonist. Excluding some games like Medal of Honor where it's a "reenactment" (a very incorrect one) of a war where only men fought, or a game specifically designed around a traditional male or female role in society, I wouldn't care to play a male or a female either way.
A good example of this is in Pokemon. I was a male in R/B/Y/G/S, so when Crystal finally came around, I chose the chick specifically because I had never played a chick before. It changes the game absolutely nothing, but it adds a new element to the game if for nothing but practicality reasons. Any time I crack open a new game I always start as a male because I am one, but I usually start my second game as a female just so it's a little more of a new experience, but I don't enjoy any game more or less on the sex of the character I'm playing.
I think the best example of this is in the Elder Scrolls series. From the original, Arena, throughout Daggerfell, Morrowind, Oblivion, and in the new one coming up (hopefully), you can choose to be a male or a female. And this game, you explore and fight and slay demons and/or slay innocent civilians and do so many things that are traditionally "male" things. Yet you can always be a female. And I've played plenty of female games and enjoyed them all.
And there do concern this issue; there are female characters who will flirt with a male protagonist and snob a female protagonist, and vice versa. But it's always a great game, regardless of the sex of the character.
I think that things that are already established, like a male Link and a female Samus and such, should ALWAYS stay the way they are, and things like war games based in the past should stay the sex that would be more accurate, but just about anything and everything else would make no difference to me whether the lead was male or female, or you get a choice, or you switch between multiple characters, or whatever. Just make a good game, and make a good character, and the rest is just cake.