While on cruise there is no signal with modern 3g, also you go too fast to lock any tower so you don´t get the interferences. With old analog cell phones it was pretty usual to maintain signal and talk even at 30k feet (they affected flux sensor of the compass though).
This heavy transmission from tens of phones at the same time may or may not cause radio communication interferences (the same one you hear when your phone is close to the car radio annoying but not lethal), system computers reboots or complete loss of flight computers (and this can be very scary in bad weather, heavy traffic airport and close to the ground). This has happened to me while in a landing in Paris, not something that I would recommend. Also a friend of mine had all the flight computers, alarms and lights going wild while trying to land at Madrid too. Usually is less dramatic than that, and only a computer or system resets, but you don´t know when or how you are going to face it and how bad will become.
The problem with flight modes is that a significant portion of passengers don´t know how to set it. Some of them don´t even know how to power off their phones, with the stewardess having do it 2 or 3 times each flight(improving lately, it seems people begin to know their devices).
Maybe with an 3g antenna inside the plane, all the signals could be kept at low levels and this way be able to avoid interferences to the flight equipment.