I just answered my own question at wikipedia:

"The etymology of the word could be from Old French villein, in turn from Late Latin villanus, meaning serf or peasant, someone who is bound to the soil of a villa, which is to say, worked on the equivalent of a plantation in late Antiquity, in Italy or Gaul. Poverty was equated with moral turpitude; villains had to work their way up the social ladder. Thus usually the word villain suggests that the villain's schemes stem from their own moral indifference or perversity of character."