At the end of chapter 23, Jem says that he understands Boo Radley better now. How has the trial helped him understand Boo?

Jem is adamant that Tom is innocent.  He doesn't see how the jury could possibly return a "guilty" verdict based on what he's seen at the trial.  The fact that he's wrong totally shatters his faith in humanity.  This connects with Boo in two ways.  First, since Jem has lost his faith in humanity, he understands that maybe Boo is the smart one -- if society is capable of being so horrible to someone, why be a part of it?  Second, Tom is innocent and he's wrongly targeted.  Boo, as well, has many things said about him (monster, eating squirrels, lurking outside at night, stabbing parents with scissors) and he's innocent as well.  Both Tom and Boo are connected throughout the novel, culminating in the symbolism of the title "To Kill a Mockingbird": both Tom and Boo are the mockingbirds of the novel.