I always wondered about this myself. It made the ending a tad sad because of it. I was hoping Scout and Jem and Boo would all become buddies and visit each other; it's sad that Jem never got to see Boo at all. Scout acknowledges that Boo had become their friend, but they had not been able to repay him for his kindness and heroism. No doubt, Boo had served his purpose and completed his mission: to protect his two young friends from harm. Once Bob Ewell was out of the way, Boo must have assumed that the kids would not need his watchful eyes to protect them further. They were no longer the innocent little children from the beginning of the novel, and Boo had made his true intentions known.
I think sometimes when we have an isolated experience, it's meaning lasts for us. For example, teens who go to Mexico to build a house for homeless one time in their life are much more affected by the experience than the teens who live by the border and go there every summer, sometimes for work, sometimes for play.
The ending with Boo's character being held in tact, and the memory of his impact left imprinted on Scout is significant. I believe it has created more value for her regarding who he was and what he stands for. Had they become ongoing friends, the moment would not have been near as significant.
Boo was and is a hermit, he never really liked to get into people's business or be out in public or be involved. Though it is great that Jem and Scout have this guy looking out for them, once the danger is gone, they don't need him that way anymore. And I think it would have been a betrayal of Boo's character had he suddenly become a happy go lucky friendly guy. It just wasn't in his nature.
Because of this, I think it is a better ending that they don't end up becoming the best of buddies. It is more realistic and again, stays true to the character that Harper Lee created rather than just being sappy for being sappy's sake.