Atticus is sure Jem killed Bob Ewell and doesn't want it covered up. But Tate says that Jem didn't kill Ewell. Boo Radley did. As sheriff, Tate decides that Boo was saving other people's lives and doesn't need more attention. Atticus asks Scout if she understands. Scout says she does: bringing attention to Boo would be like shooting a mockingbird.
Scout realizes that Boo stays in his house because he's an innocent, unable to deal with the messiness and sadness of the outside world. Like the mockingbird, he left this house only to help others, and therefore deserves no pain or torment.