The Nazis are the bad guys. Surprised? We didn't think so. They're cruel, they execute people, they hit women, and they're working to "relocate" the Jews. Even when they're talking about their own children, which should soften them up a little, they're still incredibly scary. And to top it off, they conduct manhunts with big scary dogs—total bad guy accessories.
Here's a good rule of thumb: if there are Nazis in a book about the Holocaust, they're probably the antagonists.