In many ways, Jem is a tiny version of Atticus himself. Sure Jem deliberately disobeys Atticus every now and again, but Jem absolutely never wants to disappoint Atticus.
"I—it's like this, Scout," he muttered. "Atticus ain't ever whipped me since I can remember. I wanta keep it that way.
Jem, like Atticus, will choose to do the honorable thing even if it isn't necessarily the right thing to do or the smart thing to do. That is why Jem goes out to fight the lynch mob even though it is in direct violation of what Atticus told him to do.
Jem also has a strong moral compass. He sees clear divisions of right and wrong. Because he is that way, he assumes that everybody else is that way too. That is why he so strongly believes that the evidence will show the entire court that Tom Robinson is not guilty. Jem is completely lost, when the guilty verdict comes through. It throws his world upside down, because he realizes there is more to people than simple right and wrong.
"That's what I thought, too," he said at last, "when I was your age. If there's just one kind of folks, why can't they get along with each other? If they're all alike, why do they go out of their way to despise each other? Scout, I think I'm beginning to understand something. I think I'm beginning to understand why Boo Radley's stayed shut up in the house all this time... it's because he wants to stay inside."