Many 'planes in that area operate without transponders so perhaps the military would not concern themselves with a civilian flight on a normal flight path.
Perhaps it didn't deviate far off course and carried out a planned landing at a secure base.....there was a suggestion that a large group of computer boffins were among the passengers. Very useful people to have working for you.
An airliner packed with explosives could be a rather large step up from a car bomb......just a thought!
