I don’t think Pixar is shy at using female leads; it’s just a case of having a story appropriate for a female lead, as others have noted.
It is worth pointing out, as a sidebar, that an early story for Toy Story would have a Barbie doll get macho’d up, a la Ripley in Aliens, then leading a rescue of Buzz Lightyear from Sid’s house. The idea was scrapped because (a) it took the focus away from Woody, and (b) Mattel squelched the idea, but it does lend credence to the “girls need to be tomboys to get the lead” meme above.
I honestly don’t know. The list wasn’t meant to be exhaustive, just something I could come up with off the top of my head. My viewing habits are so far removed from the norm, I can’t judge, or even make guesses. The only movie I’ve seen in theatres for the past several years was Howl’s Moving Castle, which featured a female lead who was not a tomboy. But I am well aware that it is an exceptional movie in many regards.
Your (and fluiddruid’s) point about male leads being the default norm is well-taken. But I’m not sure it’s a matter of market factors, as you’re implying, rather than more to fluiddruid’s point about unless there’s a specific reason to make a character female (or anything other than straight, white and male) the default is for male.
I think that Pixar is more likely than Disney proper to be willing to create a female-lead movie. Certainly they’ve got a far better record for interesting female characters than Disney’s animation. (I can’t talk to Disney’s recent live-action stuff. Ain’t seen it. I keep trying to say I need to see Princess Diaries, but it’s such a low-order thing… it’ll be a few years, yet.)
I agree that fluiddruid’s point is a good one, but I think we are looking at it at different levels. She is addressing the “why won’t guys typically see a movie with a female lead” whereas I am making the point that we know that viewership is lower for female-led movied because if it weren’t, they would make more of them.
Getting back to the why, I once wanted to do a study in which I asked people to describe a typical person. My hypothesis was that most people would think of a male when I asked for a “typical person.” This, of course, is the point fluiddruid is making–men are the norm, women and minorities are exceptions. I think that it is sad that we think this way, but I also think it is true for many, if not most, of us.