How is it possible for Bruno and Shmuel to have fun together and maintain their friendship despite their circumstances?
Likewise, people ask, why doesnt Bruno try to protect his friend when Shmuel is attacked by Lieutenant Kotler?
Because he was as scared of Lt. Kotler as Shmuel was. They're young/he's the only friend.
Also question is, how does Bruno justify continuing his friendship?
How does Bruno justify continuing his friendship with Shmuel despite what his father, sister, and tutor have said about Jews? He only wanted a friend to play with and Shmuel was the only one he can talk to. Also, the loneliness and the terrible-atmosphere were also the reasons that Bruno wanted to be with Shmuel.
One type of separation the fence represents in this story, is everything Shmuel knows about the Holocaust, and the other side, is the ignorance of Bruno, and the little he knows. Another type of separation is what the people have gone through on each side of the fence.