This book lets us see through our eyes and Charlie Gordon's simultaneously. We can see when people are laughing at him but Charlie, in his childlike way, doesn't get the joke. He doesn't understand that he is a punchline and the reader feels protective and also helpless. And also angry.
His innocence pulls your heartstrings, but not as much as Charlie's desire to improve himself.
This desire leads to the experiment. As he gets more intelligent, he re-visits unpleasant memories about his childhood. His disillusions and new-found sexual desires confuse him.
It is the sex part that causes problems. From Wikipedia:
In January 1970, the school board of Cranbrook, British Columbia, as well as Calgary, Alberta, banned the Flowers for Algernon novel from the local grade-nine curriculum and the school library, after a parent complained that it was "filthy and immoral". The president of the BC Teachers' Federation criticized the action. Flowers for Algernon was part of the BC Department of Education list of approved books for grade nine and was recommended by the BC Secondary Association of Teachers of English. A month later, the board reconsidered and returned the book to the library; they did not, however, lift its ban from the curriculum.Challenges to the novel have also been successful in Texas and Pennsylvania.
This novel is about an innocent man losing his innocence, about the difference between intellectual intelligence and emotional intelligence. Between being a genius and being a grown-up. It's a fascinating, touching, unusual and provocative book.
And all they saw were the "dirty bits".