Here's the thing...
Monsters Inc was cute enough, but its main thing it had going for it was the animation of fur. From a pure animation standpoint, it could have won. BUT, the category is best animated FILM, and the film as a whole is judged. Storyline, characters, humor, pacing, etc. As an overall film, Shrek was the better choice. I think the academy voting was pretty right on in this case. Had there been a separate Oscar for animation technique, then I would have been pulling for Monsters there.
Shrek was able to reach all levels of its audience - it had the physical and slapstick humor for the kiddies, as well as the more subtle jokes and obscure references that draw in the adult audience. It was a better overall film. If you took the fact that it was animated out of the picture and just judged them as films, Shrek was the better of the two. Just as you'd judge a comedy or drama as an overall film, not as a "live-action" film. To some extent, you do need to consider the animation aspect, but it's just part of the entire package, not the be-all and end-all of the category.
I don't think Shrek was voted the winner *specifically* to slap Disney in the face, but that said, the fact that Dreamworks is making better animated films and the audience is recognizing it SHOULD be something of a slap in the face for them. It should NOT have happened, and only has because Disney is getting cheap and lazy. They could have kept Katzenberg years ago, but chose to make an enemy of him and it's coming back to bite them because Katzenberg took all his Disney skill and knowledge and is now using it to beat Disney at their own game. I say, yay Katz!
It's kind of like how Disney keeps laying off the imagineers and other companies are picking them up and doing the great work Disney is now too cheap to do. They're throwing away their market edge. Many of the animators and imagineers would have LOVED to be/stay with Disney if Disney didn't treat them so poorly. But all that talent is going to companies who actually want to do the great work that Disney pioneered.