The Doctor generally isn't a villain, but occasionally cleaves close to it. Remember the whole "Time Lord Victorius" thing? Or the other times where the only thing to keep him from doing terrible things is his companions. The Doctor has said it many times himself that when he's alone for too long he goes.... wrong.

I also think that you've got me confused with somebody else and you really should double check who you're replying to in the future. But what they said is correct. The Doctor is a deity and a terrifying existence--whether he is good or bad; hero or villain, is often down to perspective. Most of the times he comes across as good, but he is always capable of doing terrible things.