An issue could occur with navigation while you're 40,000 feet in the air, but it's unlikely. Most newer airplanes use GPS these days. You have to think about how GPS works. It's one big speed=time/speed calculation for as many as seven satellites. The GPS receivers on the aircraft need ephemeris and course/acquisition data to track your flight path and could be corrupted by superfluous data from your cell phone. A Boeing 737 doesn't need 5 miles of lateral separation, but the FAA errs on the side of caution. The NATSB has helped to set standards to keep planes in the sky, and the FAA follows their recommendations for the most part. Although most aircraft have GPS, it is not required by the Federal Aviation Regulations. It would be extremely expensive to upgrade the entire air traffic system with new equipment and retrain all the controllers.

The line of sight (pulse) radar that is used by ATC is more susceptible to interference than GPS. The FAA requires the planes to transmit a specific code number when in class Bravo airspace--the same airspace you fly in while on a commercial flight. It is possible for someone's phone or device to transmit a beacon code that belongs to another plane. It may be unlikely, but ATC doesn't want to lose you in the sky.

The reality is though, you are allowed to use these phones during flight, just not landing, takeoff or taxi. Why? Most pilots don't do a whole lot to land the plane. What I mean is they don't do a lot to navigate their plane in a landing situation. Commercial aircraft have a precision landing system, either instrument, microwave, or precision approach radar. The Instrument Landing System, or ILS, is equipped with three different types of transmitters: the localizer, glide slope, and marker beacon. The localizer provides lateral course guidance information. It is one of the most precise and sensitive navigation aids available for instrument approaches. Unfortunately, its signal can be easily reflected off of buildings, land, power lines, etc thereby creating false courses.

In an IFR, or Instrument Flight rules situation like rain, snow, fog, etc...the pilot can't even see the runway until he's too close to adjust speed and altitude. The localizer helps the pilot bring you home safe. This is the chink in the armor.