A major theme of "Flowers for Algernon" is the cruelty of using a human being as an experimental "lab rat" to advance medical science before the science is ready for human testing.
Charlie, who doesn't have the intellectual capacity to give informed consent, is urged into experimental surgery to improve his intellect. Unfortunately, one of the key figures behind the experiment, Dr. Nemur, is aging and wants one last great success before his retirement. Therefore, he rushes forward with the surgery before he has sufficiently tested the data, not taking into account the degree to which his career ambitions could do harm to a human life.
At first, the surgery is a success, and Charlie's intellect rapidly increases until he is a genius. At this point, however, he analyzes the experimental data and realizes his intellect will decline back to a mentally disabled state equally rapidly. So will the intellect of the lab mouse Algernon, whose intelligence was also enhanced by the surgery. Charlie realizes too late that he mattered no more to the architects of the experiment than a lab animal would.
Through reading the story from Charlie's first-person point of view, we identify strongly with his yearning desire to be intelligent and the joy that comes into his life as his horizons expand. We then feel the failure of the experiment as a crushing blow, just as he does. To us, he is fully human, and we therefore feel the cruelty of what was done to him.
The story is a warning to science not to get ahead of itself, written in an era when surgeries such as frontal lobotomies were done without a full understanding of their devastating impacts.