Why does Bruno say this? "'What exactly was the difference?' he wondered to himself. 'And who decided which people wore the striped pyjamas and which people wore uniforms?'"

Bruno is gradually starting to become more curious about life on the other side of the fence. As he explores the area surrounding his new home, Bruno wonders just what it is that makes the people in the striped clothes different from men like his father who wear uniforms. Bruno's still incredibly young and naive and so doesn't know the answer to his question. There's clearly a difference between the two groups of people: they look different; they dress differently. But Bruno doesn't understand just why that is.
However, Bruno does at least know that someone, somewhere must have created such a division. Bruno may be young and naive, but he still senses that there's something artificial about the distinctions between the Germans and the Jewish inmates. The Jews and their German captors are all human beings, so there's nothing remotely natural about the imposed differences between them.