The prohibition could very well be due to the possibility of RF interference. Most receivers have a local oscillator (LO) which is mixed with the received signal to produce an intermediate frequency. Some poorly designed receivers/mixers allow this LO signal to radiate back out the antenna. Here, the danger is that this signal would be mixed with the sattelite signal in the avionics GPS and produce spurious results.
If the fear is that passengers will know the aircraft position, then what will they do as inertial navigation systems become accurate enough and are incorporated into personal gadgets?