It's based on a U2 song that the creator likes and the address of the high school and also justified in a line in the actual show. From an Alloy article about the title:
For one, Tree Hill High's address is 1 Tree Hill; since it's the center of all the basketball, relationship, and time capsule/school shooting/Evil Dan intrigue, it makes sense. But the title didn't really make sense to fans, or even the CW producers, until episode 1×21 “The Leaving Song.”
Originally [creator] Mark Schwahn wanted to call the show An Unkindness of Ravens, but The CW (then The WB) didn't want to alienate fans with a show only about basketball. (Schwahn got some vindication when he had Lucas write a bestselling novel about his adolescence, titled An Unkindness of Ravens.) So Schwahn went to a favorite U2 song off their album The Joshua Tree. But after executives asked about the meaning of One Tree Hill, he inserted this line into [episode] 1×21:
Karen (to son Lucas): There is only one Tree Hill—and it's your home.