As you mentioned, Joe Chill is a mugger. Since you tagged nolan-batman-trilogy, i'llI'll quote the Wikipedia entry for his priorities in that series:
Chill claims to have been "driven to mug" the Waynes by poverty
Joe Chill isn't a serial killer. His goal is money/valuables not murdering powerful people and bringing the police down on him. Furthermore, I expect that a prison sentence for murder in Gotham is much longer than it is for mugging/robbery.
Joe shootsshot Thomas and Martha Wayne during a physical struggle after he attemptsattempted to steal Martha's necklace. It's at this point that Joe becomes loses control of the situation, panics, and shoots Thomas and Martha. At this point, Joe is standing there with 2 dead bodies, a wallet, and Bruce. Joe has what wantedhe wants (money), so now it's time to get out of here before the police show up. Bruce is no immediate threat; he is a child that couldn't threaten Joe. Bruce doesn't charge Joe or jump for the gun, so there is no reason for Joe to kill Bruce.
Going back to the point about the police; murdering a defenseless child will get much more attention than killing two rich adults during a struggle.
Acknowledging the Counterargument
Joe does have a few possible motivations for killing Bruce:
- Eliminate the witness - Bruce could give his description to the police.
- However, it's dark outside and Bruce is very young. He probably won't give a great description to the police.
- Just in case Bruce grows up and comes after him.
- This would ironically be Batman level paranoia. It's not an immediatelyimmediate threat and Joe would have to be evil to do this.
Out of universe
It wouldn't be much of a Batman story if Batman gets killed as a kid (other than Flashpoint as Richard commented).
