Because...he's hot. Why can a villain not be hot? The Master was sexy. Tom Riddle was sexy until he snake-ified himself. Lucius Malfoy had hot going on, and so did Valentine in Mortal Instruments. A lot of villains are like that, really.
In Seahome, Livier (villain) is really good with seduction and whatnot. He's from a douche bag species, is in fact the prince of that species, but he's gorgeous and fantastic at getting what he wants. That's why there's actually something that resembles a love triangle between him, my main character and the actual love interest. (But clearly it is not a real love triangle because it's still pretty obvious he's the bad guy.)