I have thought about how in Indiana Jones and the Kingdom of the Crystal Skull, the Soviet Union officials are the villains, but they are shown to be acting in reaction to existing United States weaponry and technology that is threatening their country and government. RedLetterMedia does good job of explaining this in their review of the movie.
However, their main goal is to use the titular skull for mind control against Earth's population.
Dave Anthony (or Josh Olson, I have trouble telling them apart) of the West Wing Thing is a Hollywood writer. He explained that if a writer wants to talk about an idea he agrees with but knows the studio won't like it, they'll give it to the villain. And this is the reason so many Hollywood villains make so many decent arguments. He was talking about Black Panther in particular.
That's interesting.
However, I think the average viewer will just associate whatever ideology the villain has with it being bad.