We have already established that Bones is autistic. She doesn't really understand emotions or psychology, humans have been a mystery to her ever since she was little.
This is why she started studying anthropology. Maybe if she could connect to the human experience, if she understood every culture and knew how we used to be, maybe she could understand humans now. If she could understand how we were, she would understand how we are. She doesn't trust psychology or emotions because people can lie; her parents showed her that. The bones don't lie to her, she can understand how people lived and died, but she can never find out why.
She has incredible amounts of knowledge about humans, the way we behave and the reasons we came to be, but the body could never tell her why. She became an anthropologist so she could relate to people, maybe if she studied people hard enough she could become one of them. If she read enough books, took enough classes and studied enough lives, maybe she could connect to others. The Autistic Experience, if you will. But she couldn't. No amount of studying could tell her why.
Booth taught her how to love, he taught her that you don't need an answer to everything. There is a mystery to life.
Angela taught her how to live, how to take it easy and allow yourself to have fun without feeling like you don't belong.
Cam taught her that no matter how many people think appearances are everything, they are just that. Appearances.
Sweets taught her that there is no single human experience, her life doesn't need to be lived by the books.
Zack taught her that even the smartest people can be wrong, even the smartest people have faults in their logic.
All of the people in her life taught her something that she couldn't learn from studying. You can't rationalise the human experience and you don't need to. She might not understand humans the way that she has always longed to, she can still experience what it's like to be connected and loved.