What does Atticus mean when he says that Mr. Cunningham has blind spots?
One of the main themes of To Kill a Mockingbird is the ways in which Scout's perception of people changes over time. In the early chapters, she sees the world very much as a child - people are either good or bad, friendly or unfriendly. When she sneaks out to find out why Atticus is sitting outside of the jailhouse, she is confused by why Mr. Cunningham and other members of the mob are angry with Atticus for representing Tom Robinson, particularly because the Cunninghams have also sought Atticus' help and because she is friends with Walter Cunningham, Jr.
In general, Scout sees people as more or less the same, often failing to understand how their lives have been shaped by race or class. In this case, she can't understand why Mr. Cunningham would be grateful for Atticus' help on previous occasions but be angry when he represents Tom Robinson. Atticus explains to her that Mr. Cunningham has "blind spots," meaning that he has certain prejudices and biases against African-Americans.
After the scene outside the jailhouse, the children have difficulty understanding how people they thought they knew could act so differently and become a threat. By saying that Mr. Cunningham has "blind spots," he is attempting to explain to them that people are often very complicated. Mr. Cunningham, for example, is "basically a good man" but he is also a product of his time and circumstances, which is a way of explaining his racial prejudices.
It's important to note that Atticus isn't necessarily calling Mr. Cunningham racist; rather, he is trying to impress that all people have biases and perspectives that influence their behavior.