In an interview, Sue Monk Kidd said that she envisioned the Virgin Mary as the queen bee in the story:

I discovered bees were considered a symbol of the soul, of death and rebirth. I will never forget coming upon medieval references which associated the Virgin Mary with the queen bee. I'd been thinking of her as the queen bee of my little hive of women in the pink house, thinking that was very original, and they'd already come up with that five hundred years ago!

I have pasted a link to that interview below. In it, she also discusses the image of the Black Madonna and its significance in the book.

The queen bee serves the same purpose to her hive as the mother in society does. The queen gives the hive life and purpose, a reason for existing. If each bee didn't perform its job in the hive, it would cease to exist. The hive's job is to produce honey. Without motherhood, society would also cease to exist. Lily, so hungry for a mother's love, represents what happens when a person doesn't have the love and guidance of a mother. This is what a mother produces, both life and purpose. The Daughters of Mary feel the same sense of community that the bees do within their hive.

August Boatwright has gained her understanding of life from observing the bees and other things in nature, and she imparts this knowledge to Lily. The honey the bees produce is used not only in the religious rituals of the women, but also in every other part of their lives. It's necessary for both their spiritual and physical needs. This makes the religious imagery inseparable from the nature symbolism.