First, a satellite system is easier to jam. The signals are weak and the antenna on the aircraft is semi-omnidirectional so a jammer signal can get in. By contrast, its harder to jam a radar since it has a pencil or fan beam.
Second, since the system is 'dependent' on aircraft cooperation, a terrorist can turn the on-board equipment off and become untrackable. By contrast, radars have a 'skin mode' where they depend only on reflections from the skin of the plane to track. This is not the normal transponder mode, but will defeat the attempts of a terrorist to avoid being tracked.