The imagery associated with pigs is, in general, a potent mix of lardiness and muck. I actually visited an exhibiting yesterday where the main feature was a painting of an anthropomorphised pig, with great roles of fat, with the intent of saying 'people are pigs'. There's no objective reason it has to be that way, it's just our culture, isn't it?
I haven't read much fiction, but I'm guessing the wicked-thin eyes of reptiles, along with the predatory connotations and flattened, sharp snout matches your stereotypical bad guy. I think some reptile species would make suitable good guys though, geicos, salamanders and a variety of dinosaur species could pull it off well.