The antagonist is typically the bad guy who causes the book to have some conflict. There is no way, in that case, that we can possibly leave Nazi Germany out of the bad guy club. Without Germany’s aggression, none of the events described in the diary would ever have occurred, and Anne and her family would have survived. It is because Germany occupied Holland and sought to destroy all the Jews that the Franks, van Daans, and Mr. Dussel went into hiding.
By sorting Mr. Dussel into the antagonist bucket, we’re not trying to compare him to the Nazis. Mr. Dussel is an antagonist on a different level. He’s the roommate from hell who causes Anne constant frustration. He never takes her seriously, keeps her from having any time or space alone, and is constantly criticizing her. Aside from giving Anne a root canal, this guy does her no good.