I view the story's central theme to be this: Jojo moves from an anti-semitic point-of-view to one where he is (more or less) freed of those prejudices. To use the language of philosopher Martin Buber:
I - It ---> I - You
In other words, Jojo at first perceives Elsa, the Jewish girl hiding in the attic, as an It. Note all the caricatures he shares with Elsa about what he's been propagandized to believe as part of his Hitler youth training. As he gets to know Elsa, those prejudices drop away and he starts to see her as a You, an authentic human being deserving of respect. It also helps that he develops a kind of puppy love affection for her.
With so much prejudice, racism, anti-semitism, and xenophobia coursing through the zeitgeist, the movie Jojo Rabbit reminds us - in a comedic way - of the humanity we all share.