The central irony of Flowers for Algernon is the fact that if Charlie Gordon had never had his intelligence increased threefold, he would have never been able to contextualize the horrific abuse that was inflicted upon him as a child, and therefore would have never suffered from it. This is not to say that Charlie should have never had his intelligence augmented, but it does throw into sharp relief the deliberate cruelty with which most of society, particularly parents, have been known to treat mentally disabled children. As a child, Charlie received abuse both physical and emotional, and even some abuse that bordered on sexual.
Though Charlie receives an extraordinary boost in intellect that make him all but a completely different person, it does nothing to blunt the memories of his childhood. This causes him to become mistrustful of everyone around him, and even push away Alice, the only person who has ever showed unconditional respect toward him. Due to the trauma that he can only put into perspective with his new intelligence, he cannot maintain relationships, romantic or otherwise, and is arguably more distant from people than he was as a handicapped man. This begs the question of whether or not it was ultimately a cruelty to give Charlie his intelligence, as Fanny believes.