As his name suggests, Prospero represents the forces of life, fighting the good fight against death. Or at least running from death by shutting himself up in a fancy castle so he can keep throwing fab parties. We guess that makes him the hero. He's certainly the guy in charge, and towards the end of the story, he's the only one with the guts to try and kill the Red Death. He may also be an artistic genius who represents the universal attempt of human art to conquer nature. In any case, he's the only real character in the story, so it's not like there's any other choice for protagonist.
We also take issue with the fact that Prospero abandoned all of his subjects in the midst of their suffering. So we have a hard time feeling sorry for him when he dies. Then again, maybe we're not supposed to.