There are two primary areas of concern for phone use on planes, and both of them have demonstrable effects: 1) The potential of interference with onboard avionics, particularly those designed before 1984. 2) The effect an airborne phone can have on ground systems.
http://en.wikipedia.org/wiki/Mobile_phones_on_aircraft And yes, newer planes and avionics systems are being designed to deal with this, but there's a lot of older iron flying worldwide. - John PP-ASMEL-IA
