The villain can drive the whole story, nothing wrong with fleshing them out. It makes them more three dimensional. The whole idea that the villain is 100% bad and the hero is 100% good is not only immature but makes for a very boring story.
I think it depends on the type of "villain", or "antagonist" that you are creating, and the story that they will inhabit. I quite like the idea that the protagonist is nothing to antagonist, and based on that we don't need to know everything about the antagonist's reasoning. For example, if you protagonist is stood in front of the antagonist, they wouldn't care anymore about him or her than they would the person stood next to them. It could help to make the antagonist more terrifying in that you barely know a thing about him/her/it. An antagonist I am writing at the moment is not human, and he sees humans as little more than a source of energy. Therefore, he doesn't particularly need justification for his actions beyond the reader knowing that that is his way of life. Maybe you would need more reasons from the protagonist in that case. I have also included a number of other "villains" throughout the story - villains in that they oppose the protagonist in some way, personal or otherwise. For one of them, I have planned a chapter from that person's point of view, but I imagine it would make the reader detest him more than they would if they didn't get to see the world from his point of view.
In my novel, my 'antagonist' (never villain!) is someone my beta readers—for the most part—were very attracted to. They recognised his need to be stopped from what he was doing, but could sympathise with his situation which was only partly self-created, and even 'love' him ...against their better judgement. This was a vital part of my story, and reflected my protagonist's attitude towards him as well. It makes for an interesting story if you can engender love, or ambivalence, in the minds of your readers towards your antagonist. Unless there is complete capitulation and reform on the cards (in my story there certainly isn't) your story will end with some degree of sadness, and a wish that things could have been different ...if only... This is a lot like real life, and it's fun to play with this as a writer. Of course if your antagonist exists only to test the mettle of your protagonist, then I suppose you can take a more black-and-white attitude towards him or her. But it's fun to remain in the grey area throughout. Staying grey makes for an entirely different sort of story problem.
And those who do usually try to find an excuse/reason to justify their actions, and they're usually full of self-loathing.
Replace Excuses with the word Motivation. (side note have a look at the anti hero section, hero's are not always likable)
sorry repeated my post but im being stupid and cant figure out how to delete it, so it edited the second one to say something else....uummmm so how u?