V'GER was a villain. Anything that destroys 3 Klingon Battlecruisers, Epsilon Nine, and Ilia for no apparent reason is a villain. Just because you find out it's motivation at the end of the movie, doesn't make it not a bad guy up until that point.
The Whalesong Probe in Voyage Home wasn't directing it's energy at humans exactly, but was going to kill them as a result of it's actions. Not a villain kinda like a hurricane isn't a villain.