Fairness or social justice is an important theme in both books. Atticus fights the unfairness of the racism in Maycomb when he mounts a real defense of Tom Robinson against charges of rape. He is considered by many a traitor to whites when he puts justice ahead of allegiance to his own race. Likewise, the Hubermanns fight racial injustice (the Nazis considered the Jews an inferior "race") by harboring and helping the Jewish Max Vandenburg.
Courage is also a theme of both novels. It takes courage for Atticus to buck convention and risk both his own and his children's well-being to do the right thing by defending Tom fully. Likewise, the Hubermanns show great courage in protecting Max from the Nazis.
Another theme is the move from innocence to maturity. Both novels tell the story of a young girl who has to mature quickly and face the fact that the world is a harsher and less just place than she originally believed.