In my opinion, there are three main themes in The Bean Trees: the power of friendship, the fact that actions have consequences, and human rights.
The Power of Friendship --Generally, the main characters are down and out at the beginning of the novel. As their friendships grow throughout the story, and even though the relationships differ between the lot of them, their vast loyalty to each other begins to sustain them.
Actions Have Consequences--Every single character in this novel has significant consequences resulting from a good or bad choice. These choices and consequences help us, as readers, define the characters. Taylor's choice to leave, the decision to keep Turtle, the choice not to turn friends in to the police, as well as others all define and change the lives of the characters involved.
Human Rights--This theme revolves around three specific characters in the novel: Estevan, Esperanza, and Turtle. In regards to Estevan and Esperanza, they have always been denied freedom (and even personal safety) in Guatemala and, therefore, become refugees as a result. In regards to Native American rights, one cannot deny the presence of Turtle, an abused Cherokee. These rights are often spoken of in generalities, however, because of the nature of our narrator, hence the theme of general "human" rights.
There's just so damn much ugliness. Everywhere you look, some big guy kicking some little person when they're down. It just goes on and on, there's no end to it. The whole way of the world is to pick on people that can't fight back.
Therefore, Taylor spends her whole life fighting the oppression she sees.