I don't think the plot can be boiled down to simple hero/villain roles. The Man In Black broke the rules, and received a sort of punishment for that. Unfortunately, it was an eternal damnation sort of punishment, which is pretty disproportionate given his offense. But using his powers, he spent the millennia manipulating and killing people, so he's not an entirely sympathetic character. If we take Jacob at face value, allowing the Man In Black to escape the island would be a horrible thing. So the Man In Black must be stopped.
Jacob meanwhile, sought a way to be released from his role as the island's protector, and to prevent the Man In Black's escape. So he manipulated the Candidates' lives to get them to the island, while also manipulating their lives so they would be prepared to fulfill the roles he needed them to have. In the process, he was willing to let many people die, both in the plane crash, and in conflict on the island. His desire to stop the Man In Black is noble, but his methods are not. So Jacob is also not entirely sympathetic.
The Flight 815 survivors similarly show a history of good and evil actions. This seems to be part of the show's writers' plans. No one on the show (except maybe Walt and Hurley) is entirely good or evil. No pure black and white, only shades of grey. In conclusion, the villain of Lost is the nature of humans to be evil. The hero is the nature of humans to be good. The show is about this dual nature of humanity.
