I'm not aware of any documented cases to suggest that the use of mobiles on board have ever interfered with aircraft systems, no more than there is evidence to suggest that it's dangerous to use them while filling up your car at the petrol station. But it's better not to take that chance so they prohibit their use in these situations - fair enough.
In the Ryanair case (using OnAir technology that has already been used elsewhere) the chance of such interference occuring is greatly reduced (if it exists at all) as the phones need only produce minimum power output to communicate with the on board transmitter, as opposed to maximum output to communicate with a ground station. While I would of course hope they investigate all possibilities in this crash, I personally don't feel they'll find anything untoward in this regard.
What amazes me is the disagreement amongst bread and butter pilots as to all the various A/T modes, procedures, etc for this aircraft. Surely one guy's 738 rating is exactly the same as the next guy's (ie there's only one way to fly this aircraft properly), and everyone should be singing from the same hymn sheet (though this is where different company SOPs come in I suppose)