The three main themes circle around prejudice, courage and knowledge. Atticus takes us through the theme of prejudice through his defending Tom. He shows his kids to do what is right. Both kids learn not only from him but through Calpurnia as well. They see her as a mom before they see her as their "cook."
Courage is shown in several characters. Mrs. Dubose fights her way to be drug free before dying. Atticus knows he's going to lose, yet he tries to keep Tom out of jail. And Boo risks his life to save the children.
The knowledge is throughout the book with both children. Scout learns through walking in others' shoes. Jem learns that just because Atticus proved Tom was innocent doesn't mean Tom won't be convicted. Many characters grow in this novel, but Scout is by far the one to go through the "bildungsroman" which is the knowledge and maturation over time from childhood to adulthood. Narrating the story later in life, she is able to share perspectives from both a child and as an adult.
One other theme in To Kill a Mockingbird is innocence. As the children are exposed to the town's disapproval of Atticus defending Tom Robinson, they are witness to Mr. Ewell, threatening their father, a mob of men coming to lynch Tom Robinson, the horrible treatment of Tom Robinson for feeling sorry for a white woman and the verdict of guilty to an innocent man. Dill is visibly upset because of Mr. Gilmer's treatment of Tom Robinson on the stand. Jem cannot seem to get over the guilty verdict. Scout and Jem witness their father being threatened by Mr. Ewell. With each incident their innocent eyes are opened to how cruel and unkind the world can be. By the end of the novel each child has been exposed to cruelty beyond words and their lives will never be the same again. Thus, as children grow and experience life, innocence is lost.
On the another note, Boo Radley and Tom Robinson are both innocent and it is the town who causes both characters loss of freedom and innocence.