The REAL villain was the shadowy company Dotson was working for. Nedry was just the incompetent inside man. But yes...it's always hard to classify animals as villains when they are just doing animal things.
I suppose it might be a bit of a spoiler, but they foreshadow pretty hard in his first scene. I think he’s openly a baddie by about the 35-minute mark. Hopefully this quiz doesn’t ruin any childhoods ☹️