There's no question that Adam is the protagonist of I Am the Cheese. He is the cheese, after all. The entire story is told through his eyes (even in the chapters that include a third-person narrator, that narrator knows all of Adam's – and only Adam's – thoughts). Other than Adam's parents, who are only seen in bits and pieces, Adam is also the only unambiguously good guy. We're not really as invested in the other characters. Think about it this way: when Adam's mom dies, do you feel sad for her or for Adam? That's how we know our hearts are with our protagonist.