A major theme in this novel is prejudice, and not just racial prejudice. This is a small town in the 1930s south, and despite the fact that there are some liberal folks there who believe people should be treated equally (Atticus and Miss Maudie, for example), there are still an awful lot of people who think blacks have their place and should just stay in it. During the trial of Tom Robinson, it is shown that even though progress has been made (think of how hard Atticus worked to defend Tom), they still have a long way to go when there is overwhelming evidence to acquit Tom of the rape charges against Mayella Ewell - and yet the jury still finds him guilty.
I said above that the book isn't just about racial prejudice. It's also about intolerance of any kind. Boo Radley is someone who Scout and Jem learn to respect and treat the way they would want to be treated, even though he and his family is vastly different from their own.
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Building off "pro29's" answer, I would say that another major theme is empathy. Stepping into someone's skin shows the ability to be understanding and empathetic. Similarly Tom Robinson was also empathetic towards Mayella.
Another major theme would be bravery (and cowardice). Atticus, Jem, Dill and Scout display bravery at the Maycomb jail.
To some extent "true justice vs. Maycomb law" also
Another major theme would be Innocence, how the children start off innocent, mainly Scout, however through the events developing around her and the things she learns from the people around her, mainly Atticus, for example, a major quote that Atticus says changes the way she thinks of people dramaticaly "First of all," he said, "if you can learn a simple trick, Scout, you'll get along a lot better with all kinds of folks. You never really understand a person until you consider things from his point of view […] until you climb into his skin and walk around in it." (chpt 3). They are also very innocent as they dont understand the adult mentality, for example the court case, they had little idea about the harsh racism going on.