What does Lily compare the bees to in The Secret Life of Bees?

Over the course of the novel, Lily compares the bees, their society, and their work to various aspects of her own life. Even in the first chapter, the influence of bees is clear:

The queen, for her part, is the unifying force of the community; if she is removed from the hive, the workers very quickly sense her absence. After a few hours, or even less, they show unmistakable signs of queenlessness.

This is the chapter when the reader learns that Lily may have accidentally killed her mother when she was very young. She isn't clear, and her memories are blurry, but she has lost her "queen," the one who was the unifying force of her life. In her mother's absence, she is left to T. Ray's abuse—the same abuse he doled out on her mother. So we see the implicit connection here of the queen bee's impact reflected in the loss of her mother at a young age.
In this same chapter, Lily finds a swarm of bees inside her room. When she leaves the room to get T. Ray, she finds that they have disappeared when she returns. She initially traps them in a glass jar as proof to T. Ray that she was telling the truth, but she releases them later, thinking that the bees would want and deserve their freedom. In chapter two, she faces the decision of leaving T. Ray in order to help Rosaleen and perhaps find a better life for herself as well. She finally realizes what to do by remembering her trapped bees:

But I had such a moment right then, standing in my own ordinary room. I heard a voice say, Lily Melissa Owens, your jar is open.

Her freedom is wrapped up with the bees' freedom. She realizes that just as those bees didn't realize the freedom that awaited them when she removed the lid, she has a greater freedom awaiting her that is yet to be realized, as well.