Jem actually has a couple of theories about exactly why Boo Radley does not come out of the house.  In chapter one he said that he thought Mr. Radley kept him chained to a bed.  Later Scout says Jem told her they had killed him and stuffed him up the chimney.  However, these somewhat melodramatic theories reflect the fact that Jem, as well as most of the town, think that Mr. Radley is somehow keeping Boo from leaving the house, first because of the disturbing the peace incident and then because of the scissors incident.  Thus they are all somewhat surprised when after Mr. Radley's death, Boo still does not leave the house.