Boo Radley is used to explore many themes, including the theme that you should treat people with respect rather than intolerance or prejudice.
Boo Radley is an important character in the book, although it is true that he does not appear often. From the beginning of the book, the child characters are focused on Boo. This is to frame the story, and let the reader know that the story of Boo Radley is important. In the beginning, we are introduced to prejudice and intolerance in the town of Maycomb through the rumors about the Radleys. Boo is regarded as a monster, and the children act out his story in the yard. Atticus tries to encourage his children to be respectful to the Radley family and Boo in particular.
The prejudice and discrimination faced by Boo foreshadows the larger societal problem of racial prejudice that we see in Tom Robinson. With Tom's case, the story moves beyond the childlike innocence of the theme we saw in Boo and moves to the deeper, darker realm of the deep-set societal prejudice that Tom faces. As with Boo, the children learn that someone is not less than a person just because he is a member of the "other" and a victim of society.
At the end of the story, the two plot lines converge. This is where the theme is solidified. Ewell, the person who truly is bad, tries to attack Scout and Boo saves her, killing Ewell. We learn that Boo is kind, gentle and shy but also brave enough to leave his isolation to reach out and help Scout.