Prejudice is caused mainly because of what our parents think and what their opinions are. Children are very much influenced by their parents and parents teach their children so whatever the parents think, the children would most likely agree. Also, Bruno being a German family, many, not all, Germans were siding the Nazis and they encouraged what they were doing.
Prejudice is also highly affected by what people around you think, like peer pressure. If a group of people think something, another person is most likely going to agree. Another reason people would be prejudice is because they have a leader. Hitler didn't like the Jews and many people followed his lead, hence the amount of people against Jews.
Bruno and Gretel were influenced by their father and they believed that Jews were horrible people. Bruno was the only one who actually interacted with a Jew for a longer time period and he knows that Jews aren't actually bad people. This shows that the opinions of people most likely revolve around someone else's opinion.