Usually villains aren't villains just for the sake of being evil. In One Piece they are usually megalomaniacs or simple greedy bastards, and the underlings of such characters. Of course there are a few exceptions like Moria and the former lord of Chopper's island. So, the bosses aside, it's perfectly natural the underlings aren't necessarily evil at all beyond having followed an evil person.

However, aren't the skyfish riders slavers? I'm not sure such people will be made good even by One Piece...