I participated in UK classified autoland (automatic landing) projects during the sixties. Autoland is a system designed to completely control an aircraft from middle altitudes to precise touchdown on runway at a distant airport, with zero intellectual or physical input from pilots. Nowadays entire integrated aircraft systems are controlled by computers 1,000+ times more powerful than we had then.
It is 100% possible to take over the flight control computers of the 747, 757 and 767 if you have the right access codes and op frequency. The computers can also lock out radio communications including IFF transponders. Under these circumstances the pilots would be completely powerless, able only to look out of the window to see where they were being taken.
In the mid-nineties Lufthansa, appreciating the potentially catastrophic effect of "boffins" hijacking their Jumbos by remote control, and assisted by the Luftwaffe, stripped out the American computers and replaced them with classified German equipment. At the time I thought Lufthansa's investment extravagant and slightly paranoid. Now as I look at the video of those planes crashing into the World Trade Center, I marvel at the foresight of a few clever Germans.
I suggest you read The Millennium Project. Believe me when I say that what the author writes about is entirely possible, and far more beyond that. Think of radio controlled model planes and you might get close to the nature of the technology used.