Scout points out that it was the only time that she ever heard Atticus say something was a sin. This illustrates how passionate Atticus is about the subject.
Tom Robinson is definitely a good example because he has been framed due to his race. He is a completely innocent, good man who did nothing to hurt anyone but who is now, in turn, being hurt by society's twisted beliefs. He is a victim of something that he did nothing to deserve. Like a mockingbird that will draw no negative attention but is shot, Tom is being "shot" by his society and it looks pretty hopeless for him.
Boo Radley is also a good example for similar reasons. Boo has done nothing to evoke suspicion, yet society is judging him by what they THINK they know; outside appearances are also guilty, like in Tom's case, for how Boo is treated by others. In reality, Boo is also a gentle, innocent man who has fallen victim to the "shot" after doing nothing to deserve it.
The title is meant to refer multiple people as examples of the mockingbird. At various stages of the book there are different, less obvious, “mockingbirds” falling victim to society. Boo and Tom are the most obvious. Atticus himself can also be viewed, at times, as a victim of society’s expectations and beliefs. The work as a whole aims to demonstrate how many are willing to attack/hurt others based on no real reason except the cruelty of perception.