Jon's dad had to face the fact that Jon is different than him, and that Jon was not going to change, no matter what. Jonathan tried to stop flying in order to make his dad happy and be more like the Flock. But, one day, he learned a new flying trick, and he breaks the promise to his dad and himself. He flies 8000 feet in the air, and just doesn't care because it felt right.
(Continued)
He was a very cool character in this book because he teaches that being different is okay. Eventually, he is recognized for this quality, and is made a leader and allowed to teach others in the flock. This would not have happened if he had not taken risks.