Some of the more sophisticated supervillains do have noble goals, but suffer from nothing more than an imbalance of coefficients in their utility function. For example, a non-supervillain who wants to prevent nuclear war might undertake public awareness campaigns, invent anti-ICBM defence technologies, run for office in order to implement disarmament policies, etc. A supervillain would enslave humanity instead, then rule with a titanium fist, ruthlessly eradicating any humans whose actions could conceivably increase the probability of nuclear war.

EDIT: the paragraph below was changed in order to avoid running afoul of the commenting policy.

The interesting thing about such villains is that their methods are often highly effective, and thus, potentially entirely justifiable. Let's imagine that, after careful reflection and lots of Bayesian updates, you became 99.999...% certain that you could usher the world into a peaceful and prosperous future simply by unilaterally killing off a few troublemakers (super-powered or just super-nasty) with your laser-eyes. Well, that, and installing a Panopticon-grade surveillance system to ensure that you don't miss any troublemakers by accident. And, naturally, instituting a massive awareness campaign to reduce the chances of troublemakers arising. Would you be able to convince yourself to not do all of that ?