What you ear is the GSM signal from the phone. It have nothing to do with the TomTom. The TomTom doesn't need to be in the car or even close for you to ear this. The difference is, when you have the TomTom connected to the phone to get the LIVE services, the phone is transmitting way more often and at stronger level than if it would be only in voice mode so, you will notice it more.
I suggest trying to move the phone. Often, 6 inches will make a difference. If the phone is right above/below the radio, there's your problem. Put the phone towards the back in the center console, in the door compartment, anywhere where you can safely reach it while it's as far away as possible from the radio/car antenna.
Also, sometimes it's the speaker wires that catch the signal. Trying to stay away from speakers might help.
Last, the stronger the phone transmit, the louder the sound will be. You could place the phone close to the car's roof, let's say on the sunvisor. This way, the phone have a clearer "view" of the radio signal so it will transmit at lower power. Don't do this if the radio antenna is in the front windshield: it could make the problem worst!