In my opinion, Lee presents the ideas that everyone is susceptible to prejudice as both offenders and victims.
Lee exposes the town of Maycomb as just as prejudiced as Hitler when she positions Scout to report on the ways of Mrs. Gates. Mrs. Gates expresses that Hitler was such a bad man because he didn't want to give the people a say. He was a dictator. What goes on in Scout's mind is that the town of Maycomb is doing the same thing to black people. This is a moment of revelation to Scout.
Furthermore, Lee uses the towns judgments of the Ewell family, Boo Radley and Tom Robinson to demonstrate that it doesn't matter if you are rich or poor (I think the Radley's must have been well-off at some point) or black or white. People just might hate you for being who you are. That is inappropriate of us to do and we should remember this story for that reason.
In terms of effects... look at what the ultimate results were for each of the characters I mentioned. Tom ended up dead. Boo ended up a hermit because he was first scared to come out because of his father's feelings about reputation. Later, I think he remained inside as Jem said, "Because he wanted to." Mayella would have loved to be in a better situation... that's why she grew her red geraniums of hope.
There is a great quote worth digging for in reference to this question. It's says something to the effect that there are all kinds of people in this world who don't agree with each other. Scout says she thinks there are just one kind of folks. Folks.