military radar techs, civilian radar techs, Air Force pilots, air traffic controllers, and the flight crew don't work for the FBI.
People who apply conspiracy theories to the Cooper case don't realize that Cooper wasn't special. There were 150 skyjackings in the previous four years over American skies. He was the first successful parajacker, sure, but much of his success was due to being first. The FBI quickly adapted and every parajacker who came afterward were apprehended.
The Cooper skyjacking was nothing more than a clever bank robbery. Even today with modern crime fighting techniques and forensics, the FBI only solve 60% of bank robberies. There didn't need to be a conspiracy or cover up for Cooper to have successfully eluded the FBI for all those years.