When Ender first takes his new army into the battle room, it seems Ender treats Bean exactly the way Graff treated him. That is, he singles him out because he is obviously much smarter than the other kids. When he does this he notices the others' resentment of Bean. He thinks to himself, "Why am I doing this... Just because they did it to me, why am I doing it to him?" (161).
There is a difference, however, in the way Ender treats Bean and the way Graff treats Ender. While Graff's treatment of Ender requires secrets and manipulation for Ender's good and success, Ender (sooner rather than later) reveals to Bean exactly how much he knows. The end of chapter 11 shows a conversation between Bean and Ender in Ender's commander room. "Bean looked at him and realized that the impossible was happening. Far from baiting him, Ender was actually confiding in him" (197).
Ender realizes two things when he meets Bean. First, he realizes Bean is smarter than the other boys, and smart in ways that he himself is not. This is why he puts Bean in charge of a special toon that comes up with crazy but genius ideas for winning battles. Second, he realizes more fully that the other armies, the other children, are not the enemies. He believes the teachers are. Bean is the first soldier who is probably as smart as Ender, and in meeting and commanding him, Ender gets a greater perspective on the bigger picture. Though he maintains his authority over Bean, unlike Graff, Ender empathizes with the boy and shows Bean this empathy. Because of this, he is more successful with his army, and later, at Command School, has built a trust with Bean that ends up saving him. Graff's relationship with Ender, on the other hand, requires mostly blind trust and hope that everything will turn out okay.