Do you consider Polyphemus a villain?
I assume you are talking about the Cyclops from the Odyssey.
It is pretty hard not to consider Polyphemus to be a villain, given what he does. When he finds the men in his cave, he shows them no mercy and no humanity, even though he is the son of a god and a nymph (so he's not just some animal who can't help it). He starts to kill the men. Not only that, he uses them for food. So he is going beyond just defending his home.
Anyway, here's a being who is eating people and then trying to kill them out of spite when they escape. It's hard for me to argue that he's not a villain.