The dangers of intolerance are all throughout the novel. Let me give you two examples.
First, we see religious intolerance in the character of Boo Radley's father. Miss Maudie gives background information about Mr. Radley. She says that he was a religious fanatic who shunned all pleasure. Her point is that she felt badly for Boo, because he grew up in such an environment. Here are the words of Miss Maudie:
“Foot-washers believe anything that’s pleasure is a sin. Did you know some of ‘em came out of the woods one Saturday and passed by this place and told me me and my flowers were going to hell?”
In a word, excessive religious commitment damaged Boo.
Another type of intolerance is racism. We see this most clearly in the trial of Tom Robinson. Most of the people in Maycomb cannot see that they racist. Atticus appropriately calls it a disease. He says to his brother these words:
You know what’s going to happen as well as I do, Jack, and I hope and pray I can get Jem and Scout through it without bitterness, and most of all, without catching Maycomb’s usual disease. Why reasonable people go stark raving mad when anything involving a Negro comes up, is something I don’t pretend to understand...
This intolerance leads to the death of an innocent man, Tom Robinson. Moreover, the people are so blind that even after Tom's death, they cannot see that an evil has been perpetrated. They simply go about their merry way.