I would say that the Nazis are the primary antagonist. Lt. Kotler is a good example of this. Bruno has nothing but disdain for the manner in which Kotler carries himself and has even less respect for him when he abuses Pavel in such a callous and cruel manner. Bruno constantly questions the Nazi condition of absolute power. The questions that Bruno asks to himself, to Gretel, to Herr Liszt, and the thoughts that form his being are decidedly against the Nazi rise to power. Bruno's willingness to don the "striped pajamas" is reflective of how he displays resistance against the Nazis. In the sacrifice of his life for his loyalty to Shmuel, Bruno offers his own defiance to the antagonist embodied in the gas chamber and the machinery of death. Bruno's courage and sense of resistance in a world where so many capitulated and conformed to the embodiment of evil is what makes the Nazi ideology the faceless enemy against which Bruno wages war. He might not know that he is waging a war against the Nazi ideology, but the fervor with which Bruno pursues that which is right is distinctive. It is because of this that Nazi ideology is the antagonist.