The problem with iPhones (and iPads) is that if you put them into flight mode, this also disables the internal GPS.
It's likely that if you've gone to the trouble of mounting your iPhone in a cradle and supplied power to it that you're going to want the GPS working!
So you have three choices.
1) Don't put it in flight mode
2) Take the SIM out (although you'll still get occasional chirps)
3) Put it in flight mode and use an external GPS
I get no interference at all from my phone - in my aircraft, it seems the key is to simply keep it away from the headset cables.