Though I agree that animals can't really be 'evil' in the sense we know, there are definitely reasons why certain species are more frequently cast as the villain. For one thing, it's human nature to project emotion and motives onto animals (heck, people project ulterior motives onto their laptop when it doesn't work right). Dogs aren't able to feel guilt in a human sense when they do something wrong, only fear that their owner is angry, but they look like they do because that's what pacifies their human, and you always hear people saying things like 'he feels guilty, he knows what he did.' Likewise, wild animals probably don't have the capacity to do something with malicious intent the way a human would, but they often do things that, if they were human, would be seen as evil or sociopathic behavior, and we easily see it that way because our brains are wired to. Where a fox sees an easy target to provide food with minimal risk to itself, a human sees a cute little innocent bunny frolicking happily in the meadow, about to meet a tragic early end at the hands of a conniving, ruthless carnivore. It's even more so with coyotes and other animals who might take beloved pets, even though, of course, the coyote can't know or care whether its food belonged to a human.
Pair that with the fact that most stories need a villain or antagonist, along with the fact that we've been hearing about sly foxes and big bad wolves for centuries. If you have a fox character and a rabbit character, it only makes sense for the rabbit to assume the fox might be thinking of eating it, making it the obvious choice for villain over its harmless vegetarian counterpart (how would you even write an evil rabbit in a realistic RP? "Muahahaha, I'm not going to let the fox catch and devour me, and it will starve! MUAHAHA. NOW I'M GOING TO EAT THIS GUY'S LOVINGLY TENDED RHUBARB PATCH. I'M SO HARDCORE).
Not that it isn't really annoying when you're just sitting there on a fox/crocodile/lion and a prey animal randomly tells you off for being evil just because of your species (it's also kind of rude, honestly, and brings up a whole other issue of confusing OOC with IC), but it's kind of what people are naturally inclined to do.
Sorry, I should probably stop writing little mini-essays in Game Discussion threads...