Out of idle curiosity I just took inventory of my video game collection to see just what the ratio of male to female protagonists came out to, and out of the 115 titles where there isn't any choice of gender (or where gender is pretty much irrelevant like (most) RTS titles) only 11 of those featured a female protagonist.
But of those 104 games with male protagonists, you can probably excuse titles like Sam and Max, Loom, Grim Fandango, or the Monkey Island series without anyone minding much, so that's 7 gone (97 left). Then you have the WW2 FPS titles, where it would be completely thematically inappropriate to insert a female protagonist, so that's another 7 gone (or 8 if you count Iron Storm, which is an alternate reality where they are still fighting WW1), so we're down to 90. And you can't really fault a game for using a male protagonist when it's using an established character who is male (Indiana Jones, Wolverine, etc), or fictionalizing a real person (Soldier of Fortune's John Mullen) and games like Max Payne and Serious Sam have the main character's name in the title, so it would be silly to expect the option to play as a woman in those (though Max Payne 2 does feature segments where you do in fact play as a woman whether you wanted to or not), so you can probably give those all a pass (that's another 12 gone, 78 left).
I would also consider titles like Sanity: Aiken's Artifact (Ice T), Tachyon: The Fringe (Bruce Campbell!) and the Splinter Cell series (Michael Ironside) to be mostly exempt as well as the respective actor's portrayal of the main character pretty much makes the game what it is (that's another 4). And is anyone honestly going to fault the Hitman series for sticking with 47, or Thief for using Garrett?
The Legacy of Kain series is another I would toss out as Kain and Raziel ARE the game, so that would bring us down to 64. Anachronox is an eastern-style RPG done by western developers that parodies itself and everything else with a 'hard-boiled' detective as the main character, ergo can't see that really working with a female protagonist since the inspiration was old noir films (but in space!), Armed and Dangerous would have to be completely re-written (probably for the worse, as it is hilarious), Bioshock has you playing a mute that might as well be genderless so the option to pick a character you then never actually see much of seems like needless frippery, Clive Barker's Undying is set in the 1920s with a protagonist who was a former soldier during the Great War, Contract J.A.C.K. was a spinoff of a series that featured a female protagonist (and unlike N.O.L.F., he's not characterized at all) so that probably doesn't count, Descent has you basically playing the ship, and until the 3rd game the protagonist never actually appeared on screen (just a tiny bit of text in the first and some voice-work in the opening/closing cutscenes in the 2nd), Doom 3 is another case of the mostly invisible and irrelevant main character where the option to be female would be essentially meaningless, same thing with System Shock 2...
I would go on, but the point is that the bulk of the titles I own that force you to play as a male protagonist either couldn't really accommodate a female lead without becoming a different game entirely since the character was a very large part of what made the game good, or it would honestly make no difference and be kind of pointless for the developers to bother. The games that I own that would work with either gender tend to have that as an option.