I don't really think the Academy has an inherit bias against computer animation, I think their problem is the perceived (and not entirely deserved) "kiddie" aura of Pixar's films. I actually think Beauty and the Beast is the best of Disney's hand-drawn animated classics, but discounting that, what separated it from much of the rest of Disney's catalog was how "mature" it seemed in comparison. Granted, you had the comic relief of the furniture servants, but if you look at the relationship triangle that forms between Belle, the Beast and Gaston, it's some pretty weighty stuff. I'm not saying that's its a better movie and more Oscar-worthy because of it (I think Pixar has made three movies that all surpassed B&tB, Toy Story, Finding Nemo and The Incredibles), but it's certainly more Academy-friendly, much like how a performance of a noted historical figure with a foreign accent often gets more attention that it likely warrants. The Academy thinks Pixar films are for children, and while they'll probably admit that they are great films, they think they aren't worthy of a Best Picture nod because of that target audience. I think if another animated film is going to follow in Beauty and the Beast's footsteps in the future, it's going to be something in more like Persepolis or the Miyazaki library.
Basically, just copy all the theories on why The Bourne Ultimatum managed to get a lot of love from the Academy last year without a Best Picture nomination, only substitute "too kiddie" with "too action-y."