In The Boy In The Striped Pajamas, does Bruno get along with his father in the end?

Bruno and his father do not have an open, affectionate relationship. Instead, Bruno's relationship with his father is rather like that of a subordinate with his superior. Bruno's father treats his son as if he was one of his soldiers; he expects instant compliance from Bruno and conduct befitting the son of an important man. The two do not get along very well.

Although it is expected that a son respects his father, Bruno's father...

Bruno and his father do not have an open, affectionate relationship. Instead, Bruno's relationship with his father is rather like that of a subordinate with his superior. Bruno's father treats his son as if he was one of his soldiers; he expects instant compliance from Bruno and conduct befitting the son of an important man. The two do not get along very well.

Although it is expected that a son respects his father, Bruno's father expects more. Throughout the novel, Bruno's father makes it clear that he wants his children to understand and support the Fuhrer's goals. Everything is subject to the Fuhrer's whims and plans. However, Bruno's father is disinclined to reveal the nature of these plans to Bruno. In fact, he takes great pains to hide Bruno from the savagery the Nazis are perpetrating against their Jewish prisoners. 

Because Bruno's father expects unquestioning obedience and loyalty from Bruno, the pair do not have an especially amiable or affectionate relationship. Also, because of his cold, detached manner, Bruno's father is never admitted into Bruno's confidence. This state of affairs results in eventual tragedy.

Toward the end of the novel, Bruno is afraid to reveal how much he actually knows about the Jewish children's plight in the camps. Bruno's father eventually decides that Bruno will return to Berlin with his mother and Gretel. Bruno never makes it to Berlin, of course: he dies with Shmuel in the gas chambers.