He's a villain because he's trying to replace the hereditary caste by violence, and by consuming them. The tension is there outside of him -- and Mr. Incredible is a bit of an arse to Billy at first -- but it's his means, not his ends, that are the problem.
We see this at the start of the film where Mr Incredible and his friend get tangled up in a rescue operation in a burning building despite having been pretty firmly rejected by baseline humans they're attempting to help, if I remember right one of them literally gets frozen alive by Mr Incredible's friend as they escape which is rather violent. We also see it when he throws his insufferable boss through several walls in a fit of anger, which is a display of his ingrained violent nature and lack of control over his superhuman powers which presents a threat to innocent bystanders. It's might-makes-right with a veneer of heroic respectability over the top, their true nature is very different from the nature they present to the public.
Either that or I'm reading way too much into a film that's mostly aimed at kids!