I think that one of the strongest and most effective themes from the book is the idea that discrimination and hatred have to be seen as moral and political wrongs. I believe that this is evident in the work in a couple of ways. One such way is that Bruno himself becomes a shining example of how the thematic statement of hatred and discrimination cannot be tolerated. His embrace of Shmuel, his loyalty to their friendship, as well as his questioning of why the present system is the way it is are representative of both his character and why he believes what he believes. Bruno is able to withstand the pressure from his sister and his father in his befriending of someone who lives in "the striped pajamas." Bruno ends up sacrificing his life for his ideals, something that members of his family come to understand later on in the narrative. The ending is one in which one fully comprehends the thematic meaning of being able to stand up against hatred and discrimination. These become evident realities out of the themes of the work and in this, one can see a thematic statement about the text emerge.
I'm not very good at writing long answers, so this probably doesn't count as a very good response, but I'm pretty sure that it's about the Nazis.