Pretty simple, right? The title refers to someone who has stolen lightning, and that person is… Oh wait, now it gets complicated. While our protagonist, Percy, does show up in the Underworld with Zeus's stolen master bolt in his backpack, we later learn that Luke is the real thief of the master bolt (and of Hades's helm of darkness). Luke is the lightning thief.
The theft of Zeus's master bolt is the reason why we are reading this book at all; it's the central conflict of the story. Zeus is practically spitting blue jelly beans because of this theft, and he's causing huge storms everywhere. Since Poseidon has recently openly claimed Percy as his son, Zeus is:
Furious that Poseidon broke the oath that he and his brothers made after World Word II, pledging not to have any more kids with human women.
Even more furious because he thinks that Poseidon convinced Percy to steal the master bolt so that he (Poseidon) could have the Cyclopes make lots of replicas of it in their forges, giving Poseidon weapons of mass destruction.
Luke is one interesting little dude. He goes under the radar for most of Percy's quest, serving simply as a friend and occasional confidante to Percy. Underneath his layers of friendliness and demi-god skill is a kid who feels rejected and embarrassed by his dad, Hermes. Luke represents the dark and tragic side of being a half-blood – sometimes it can be devastatingly lonely. We turn the spotlight on you and ask you why you think Luke is the focus of this title and not Percy?