Charlie is chosen for the experiment because he is a hard worker who desperately wants to learn, despite the many setbacks and limitations he encounters. The researchers know this because Ms. Kinnian vouches for him.
As Ms. Kinnian says, and as Charlie writes down before his surgery, “dont be scared Charlie you done so much with so little I think you deserv it most of all."
One also has to wonder if Charlie is chosen for the surgery because he has no friends or family to object to the researchers’ incredibly unethical and morally dubious tactics. Since Charlie’s family abandoned him and he has no friends interested in his welfare, Charlie is an easy target for the researchers. Because of his mental limitations, Charlie cannot fully consent to the surgery, and therefore needs someone to guard him and guide him in this decision.