Rowdy flips out on Junior because he thinks that Junior has betrayed him.
In the book, Junior and Rowdy are best friends. However, when Junior announces that he will be attending the Reardan high school, Rowdy loses his temper. He accuses Junior of having a superiority complex. Rowdy is upset because he thinks that Junior is rejecting their Native American heritage. If we refer to the text, we get a clear description of Rowdy's pain. After hearing about Junior's plans, he erupts into a keening scream and eventually punches Junior in the face.
Rowdy's reaction certainly brings to pass Mr. P's prediction. Early in the story, Mr. P has a conversation with Junior after the latter throws a book at him. During the conversation, Mr. P advises Junior to leave the reservation. The older man contends that Junior will never make anything of himself if he stays. He tells Junior that every Native American who has ever stayed on the reservation eventually gives up on life. Mr. P doesn't want Junior to share their fate.
Mr. P particularly doesn't want Junior to become like Rowdy. The older man predicts that Rowdy will become "meaner and meaner" as time progresses. He tells Junior that Rowdy indulges in physical violence because he has given up on life and wants others to feel as bad as he does. Mr. P's words prove prescient when Rowdy later beats up Junior for professing a desire to leave the reservation. Instead of being pleased for Junior, Rowdy becomes violently angry. Essentially, Rowdy's inferiority complex leads him to despair. In his despair, he resorts to violence as a means of salvaging his self-respect. When Junior tells him about his plans, Rowdy flips out because he truly believes that his best friend is betraying him.