It was nominated in that category because that is where the filmmakers opted to make it eligible. A filmmaker can say what category they want their films considered for in terms of nominations, then the nominations come out, and then the Academy votes. That's how it works. Didn't you ever wonder why Fahrenheit 9/11 wasn't nominated in the Documentary category? It's because Michael Moore didn't want it considered in that category. He wanted to give it a chance to be the Best Feature Film winner (and the first documentary to do so). So he declared that he wanted it considered in that category as opposed to the Doc cat. Nominators didn't agree that it was worthy and, so it never received a nomination.
If Brad Bird, Pixar, and Buena Vista had so chosen, they could easily have done the same thing with The Incredibles. But they were smart and realized that it didn't stand a chance against the other likely nominated films and wisely chose to have it considered for the Best Animated Feature category. Which it won. That's how the Oscars work.
Just remember when you bitch about "The Academy" and it's nominations and voting, you are bitching about people like Brad Bird who is one of the voters. I think Tobey Maguire (Spider-Man) is a member as well. The very people that are in the movies you want nominated are those that are voting.