This is actually not an isolated incident (Kung Fu Panda beat Wall-E quite roundly a couple of years back), and neither is it without reason. Disney last year announced a boycott of the awards. They identified what they saw as a bias in the voting members, had a disagreement with the organisers and withdrew from taking place in the nomination and voting.
There was no formal comeback on this, and Disney Pixar films remained as eligible as they had ever been. Now, though, they'd have a nice, clear excuse for losing – of course Dreamworks films would be likely to win when the studio's animators had the lions share of votes.
Here's how the gongs were actually shared out this year: Best Animated Feature, Best Animated Effects in an Animated Production, Best Character Animation in a Feature Production, Best Character Design in a Feature Production, Best Directing in a Feature Production, Best Music in a Feature Production, Best Production Design in a Feature Production, Best Storyboarding in a Feature Production, Best Voice Acting in a Feature Production, and Best Writing in a Feature Production all went to How To Train Your Dragon.
Meanwhile, Best Animated Short went to Day and Night and Best Character Animation in a Live Action Production went to Alice in Wonderland.
The Winsor McCay award was presented to three animation industry leaders – Brad Bird, Eric Goldberg and Matt Groening. Bird and Goldberg wear Disney colours, so maybe we can put another couple of ticks in that column. As for Groening, I guess he's the third way.
I'd be interested to see if and when Disney Pixar reverses its decision on the Annies and allows its staff to vote again.