There is much controversy surrounding this novel due to the "revisionist" history presented. It has been sharply criticized by noted Rabbis for presenting the Holocaust in an unrealistic way. However, it is a novel, so it is not intended to be truthful. Nevertheless, do you think it is problematic to present such horrid events such as the Holocaust in a lukewarm light, even if it is fictional? Good question.
Critics take issue with the fact that boys of this age (8 or 9) would be in a death camp. If children could not work, they were shot or gassed immediately. Also, the fences surrounding the death camps were electric, so it is unlikely that Bruno would have been able to crawl under it. Bruno's referring to Der Fuhrer as "Fury" is seen by some as unrealistic. Even a boy of this age would know that this referred to the leader of his country. I don't know -- do you think if you asked an eight-year-old boy who the president of the U.S. is, he would answer, "President Obama?" I think so. Further, for the times, would a young German boy not know what a Jew was? All around Germany, there were signs that read "Juden Verboten" -- and if the boy could read, he would probably ask a parent, "What is a Jew, Mommy?"
It is a matter of interpretation, then, whether Bruno is innocent or naive. Do you think it matters in the story? Consider this: questions of "how much did they really know?" aside, do you think that the author might have actually been trying to illustrate the horrors of the Holocaust by having a German child mistakenly sent to the gas chambers? Perhaps the author is asking the rhetorical question, "How would YOU like it if it were YOUR child?"
It is just so hard to be objective about this because the horror of the Holocaust is so intense, still to this day. So, even though the book is fiction, it has aroused some pretty angry debate.
You can read about some of this controversy right here on eNotes.