Even though different people might interpret this quote differently, to me it seems that since Charlie never got "normal" education for not mentally disturbed children, he believed in stuff that weren't actually true, and now that he became smart and started to understand and learn things more, he realizes the truth. Though to Charlie, it's a whole new field of education and can't make out what true and what's not, and everything seems to be a lie since Charlie has just discovered a new perspective of life. He is both puzzled and proud of this new accomplishment he made, and he now thinks that to learn more in college and education is to learn that what you learned was actually wrong.