The mechanism for the risk is that an intense radio transmission could induce a current in the wiring in the aircraft's systems.
Worst case scenario it would corrupt either the data being seen by the pilots or (much less likely) the commands being relayed back to the aircraft.
Even if such an incident occurred it would then take a further combination of factors for it to result in an actual problem - as Daver6 points out.
My understanding is that this is largely a historical risk from when cables were poorly shielded because no one anticipated passangers routinely carrying radio transmitters onboard.
Modern aircraft have wiring systems which are better shielded against this risk. But caution abounds and change is slow - and those are good things in the context of safety!
I don't make phone calls after the door is closed. I do generally switch my phone to flight mode.
However I did find it annoying when a flight attendant on an MH flight objected to me using my phone (in flight mode) to take a photo out the aircraft window.
Hopefully if the rules are uniformly updated to be consistent and realistic - flight mode once the doors are closed but okay to use in flight mode gate-to-gate - then compliance will be simpler.
In the meantime I continue to annoy my best friend by taking my DSLR on board for those photo opportunities.