The reality is that it would be insanity to have commercial sized jets flown by an onboard computer or ground computer. All signals can be jammed. Even the military channels. Learning how to jam them is not that difficult. Anyone with half a brain can get plans to build a gps jammer and buy the components at Radio Shack for a trivial amount of money.
There are commercially available electronics for less than 500 USD that are as small as a cell phone that will block all communication to and from the airplane.
Lets not make it easy for them to someday take out 100s of planes in one day all over the world.
