Why is Atticus so affectionate toward Jem after Jem disobeyed him?

Atticus sees Jem's true motivations for disrupting the Mob. Jem was worried about Atticus and it took great courage for him to face the mob of men. Jem had done something that Atticus always hoped his kids would learn. Jem had stood up for something worthy, even in the face of opposition and danger.