Charlie writes that all of the people that he works with are nice. Miss Kinnian tells Charlie that he'll show them all, but Charlie doesn't understand why, as he believes no one has ever done anything mean to him. Then Miss Kinnian said she had something in her eye and left the room.

Certainly, Miss Kinnian did have something in her eye: tears.  She was upset, because she knew where Charlie was coming from and where he was headed.  She knew that he had spent many, many years believing that people were innately good and that everyone was his friend.  However, as Charlie got smarter, he was going to find out that not everyone was as nice as he thought.  She already saw that people often treated mentally handicapped people more poorly than non-handicapped people, and she was concerned about innocent Charlie learning this world truth as well.