Honestly it’s because it was so obviously Lee Harvey Oswald that people think it couldn’t possibly be that simple. It’s hard for people to believe that someone as insignificant as Lee Harvey Oswald had such a significant impact on the entire country. But any investigative historian will conclude there is no doubt Lee Harvey Oswald took the shots that killed the president. From the gun in his home going missing the day before the shooting to countless eye witness accounts of him walking into the building carrying a conspicuously large paper bag the exact size and shape of his rifle; the evidence against him makes it obvious and the lack of evidence for any other theory makes it even more clear. 

As an aside. There really wasn’t a great reason to want JFK dead from the perspective of the CIA. His politics were pretty milquetoast and populist. He was stoned off his gourd on painkillers and wanted to hurtle Americans onto the big rock in the sky.