Charlie experiences a lot of change throughout the story, so much so that it's fair to say that he's not the same man at the end as he was at the beginning. For one thing, Charlie is so much more worldly-wise, less naïve about the ways of the world.
Having been subjected to ground-breaking scientific experiments, he's become more cynical, recognizing as he does that even what appear to be disinterested scientific advances can be distorted for selfish ends. Not unreasonably, Charlie feels like he's been used by Dr. Strauss and Professor Nemur. Essentially, he's been used by them as a guinea pig, and now that Charlie realizes that, he feels nothing but contempt for the whole process of which he's been a part.
After being chewed up and spat out by the ambitious boffins at the Beekman Center, Charlie gets his old life back. He may not be the same man as he once was, and he may be more intelligent than when he originally worked at the bakery, but at least life was much simpler then.
Even so, Charlie is anything but happy at the prospect of losing the extraordinary intelligence he acquired during the experiment. In fact, he's angry and bitter over it.