I am still wrestling with the realization that Big Pete is a cat. He was definitely the bad guy too. I always thought he was a dog, or generally the same species as Goofy, so whatever that is.
I doubt it was anything deliberate on the parts of the filmmakers. As we have shown, minor characters that were not bad guys were cats. I guess they just didn't have roles for them. It's probably just because I believe more people like dogs, and cats are necessarily adversarial to dogs (and mice). I love the Siamese cats from Lady and the Tramp, and I guess they are kinda bad guys (or creepy at any rate). I'm sure that overall Disney likes cats just fine though.