IIRC, and its been a while, is that RADAR isn't exactly hi-def, you simply see something vague which is why aircraft have transponders that reply with their ID. So if someone turns off that transponder the RADAR operators can't tell if its a plane or flock of birds or dense cloud so turning off the transponder you can sort of hide amongst all the noise (which is in part why they ground aircraft during situations like 9/11 for example).

Seems like they should make one transponder only accessible externally so they can't be turned off as I'm noticing that to be somewhat of a repeated theme in various hijackings and such.