The theme of Flowers for Algernon is that people treats others badly but that people of any intellect should deserve the same respect. For example, Charlie gets laughed at by his co-workers at the bakery, but he believes that they are his true friends. As he gets smarter, he realizes that the workers aren't really his friends and that they are only making fun of him. The workers begin to resent him and sign a petition to get him fired. Also, Nemur and Strauss (the scientist and therapist for his experiment) didn't look at Charlie as a human being before the experiment. Although the operation was to increase Charlie's intelligence, it was mainly for themselves.
Charlie evolves you see that he was still a person when he was mentally retarded. He begins to feel that the scientists are only using him as a guinea pig.
Therefore, the theme we were able to find is that a person, no matter what intellect they have, is still a person.