I think Bruno questions their viewpoints because inside he knows something doesn’t seem right. Also because he sees the way mother is acting about moving and what father and Germany are doing to the Jews. He also hears part of the big fight that his father and grandmother have about him being proud of him getting his rank bumped up.
I think Brunos instincts tell him that what his father is doing is wrong, just from the atmosphere. Like when his mother starts to cry and says they never should have had the Fury for supper. Also when he hears his father and grandmother fighting and his grandmother telling his father that he should be ashamed of what he is doing. Another way he when he arrives at Out-With and he sees the people on the other side of the fence all wearing stripped pajamas.Bruno also sees that his friend Shmuel, who lives on the other side of the fence, keeps getting skinnier and skinnier, and that he can never come over on his side of the fence to play because he is not allowed. He also sees Lieutentant Kotler kill Pavel right in front of him and nobody even tries to stop him, which Bruno thinks is very weird. I think the reason Gretel believes Lieutentant Kotler and fathers viewpoints is because she barely ever leaves the inside of her house and she is never around the Jews like Bruno is.