Coming-of-Age
Although the history of a de-segregating South churns in the background (with occasional intrusions on Lily's world), The Secret Life of Bees is primarily the story of Lily's coming-of-age. She begins the novel feeling lost and lonely, getting little to no parental guidance or involvement in her life beyond her father's fits of anger. She's so lost that she even fantasizes about what it would be like to die so she could see her mother again. Yikes.
Also, even when she tries to do something good by getting Rosaleen out of jail, her immaturity ends up showing through. As Rosaleen herself notes, Lily's escape plan is, first and foremost, about Lily, and she doesn't initially think far enough beyond herself to let Rosaleen in on her personal reasons for hatching it:
Oh . . . I get it. You ran off 'cause of what your daddy said about your mother. It didn't have nothing to do with me in jail. And here you got me worrying myself sick about you running away and getting in trouble over me, and you would've run off anyway. Well, ain't it nice of you to fill me in. (2.195)
Of course, we know that Lily does care about helping Rosaleen, but not communicating with Rosaleen about the game plan like an adult shows, well, that she's not an adult.
As the novel progresses, however, we see Lily's ability to understand and empathize with others grow by leaps and bounds. For example, when she visits Zach in jail, she wants to help right the wrong he's experienced, so she offers to write a story to put the truth out there because "it's something everybody wants—for someone to see the hurt done to them and set it down like it matters" (9.153). The gesture can't compensate him for the hurt and injustice he's experienced, but nonetheless it demonstrates Lily's growing awareness of the motivations and needs of others.
At the end of the novel, Lily gets to stay with the Boatwrights, having convinced T. Ray that she is better off there. So, when we leave her, she's happy as a clam; in addition to getting some answers about her mother that she had been searching for, she also got a whole bunch of surrogate mothers to guide and take care of her. In addition, whereas she started out flailing around trying to find a direction in life (she had been considering charm or beauty school), she is now moving steadily toward her goal of becoming a writer. You could argue that the great sign of her coming-of-age is, in fact, the novel "she" produces.