Why was JFK inated?

My mom told me that everyone liked Kennedy and was so sad when he was killed. But if everyone liked him they why was he killed? I was always taught that he was shot by Lee Harvey Oswald from a book depository, but then someone told me that he was shot from the storm drain by the CIA and that Oswald was just a scapegoat. Is it really true that he was shot from a storm drain, or was he shot from the book depository? Also WHY was he killed if everyone supposedly liked him?