surfnspy, I think you're right about animation and sci-fi. All the Sci-Fi animated fare hasn't done particularly well unless it is a comedy. I can think of The Incredibles and Lilo & Stitch as two sci-fi-infused successes, but both were mostly comedies. Treasure Planet, Final Fantasy, and Titan AE are the other ones, but none was terribly successful. I do think they sometimes make their money back on DVD.
It's hard to say why they did poorly though. I don't think it's ever just one reason. All of these sci-fi films haven't been perfect. Then again, neither have the successful ones.