1) Online sleuths believe the hijacking to have been an inside job, with Boeing having orchestrated the whole thing. However, the FBI has not given any credence to this theory and there is no evidence pointing in this direction.
2) The theory held by many in the FBI is that Cooper didn’t survive the fall from the plane. While it had been initially believed Cooper had been a paratrooper, the idea was later thrown out because of the amateur mistakes made during the hijacking.
Not only had Cooper jumped with a parachute that had been sewn shut, the one that was operable was military issue and thus not steerable. As well, an experienced skydiver wouldn’t have jumped while it was dark and storming into a wooded area shrouded with cloud cover. However, neither a body nor a parachute have been found.
3) Another theory revolves around the idea that Cooper was an experienced skydiver. While the issues noted above hint that he was not, some of his actions point in the direction he was skilled. He turned down instructions when they were offered, was aware the military chute could better withstand the exit speed of the jump and strapped on the parachute like he knew what he was doing.
This would also explain why Cooper has never been found.