In fiction, an antagonist is a character or force that creates conflict and obstacles for the protagonist, while a villain is a type of antagonist who is evil and amoral. As such, antagonists and villains are often thought to be the same thing when in reality antagonists aren't always villainous characters.
Below I will be talking about two prime examples of antagonists who are often thought to be "villains" due to their actions against the protagonists of the story when they are really just antagonists - Jackson Storm from Cars 3 and Dr. Philip Sherman from Finding Nemo.
Jackson Storm[]
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Jackson Storm is the main antagonist of Cars 3. He commits several "villainous" deeds in the film, such as bullying Lightning McQueen by saying "You have no idea what a pleasure it is to finally beat you" instead of being professional about it and giving respect to McQueen while beating him, and ramming Cruz Ramirez into the wall to prevent her from winning the Florida 500. He is often thought to be the villain, however, in reality he is just a jerk and a bully in the majority of the film who doesn't do anything evil unlike Chick Hicks and Miles Axlerod in Cars and Cars 2 respectively. When Storm rammed Ramirez into the wall, he was simply trying to prevent her from winning the race, with no evidence indicating that he intended to kill or injure her.
Phillip Sherman[]
Dr. Philip Sherman is the main antagonist of Finding Nemo. He is thought to be the villain of the story, but he is not truly villainous since he genuinely loves his niece Darla Sherman and just wants to give Nemo to her as a present. He only kidnaps Nemo because he believes he would die in the ocean. Sherman also tries to stop Nigel the Pelican from helping Marlin and Dory rescue Nemo in his office. So, despite these "villainous" deeds, he is just an antagonist and not a villain due to only wanting to give Nemo to Darla as a present.