I see a logical flaw here. There are many kinds of villains - but as long we are talking about the underground base-owning type, they usually have more or less serious intention to take over the world for themselves. Now imagine if you will: one of those guys has succeeded in clearing the way to world domination (killed the hero[es], taken out enemy leadership, whatever). Eventually he becomes a dictator, if not of entire planet then of a sizable country at least.
Now, aren't dictators known to be bad people? To uphold their own power they are willing to kill millions of people, inflict horrible torture on someone who was simply in the wrong place at the wrong time, create atmosphere of fear or hatred (or both) in their domain, hire serial rapists and other really bad people to do their bidding, and generally turning what they rule into an intolerably grim and dark place. Case in point: Josef Stalin.
What i'm trying to tell here is simple: most villains may be appealing, even sympathetic - as long as they don't do anything to you. Nothing wrong with desire to take whole world for yourself, but it also dosen't hurt to imagine how horrible it would be if someone else takes it. And then goes and kills you, your loved ones, and your dog (in a horrible, very painful way) for some minor misdeed on your part or simply for fun.
DISCLAIMER #1: Villains with "freudian excuses", anti-villains and such are partially or even mostly exempt from this.
DISCLAIMER #2: Yeah. I'm in ur thread, crushing ur power fantasies. Someone has to be Major Buzzkill and bring up the opposite side of the coin, now mustn't he?