A controversy over this flared up a few months ago. A few "belt-and-suspenders" personalities suggested that the interference with flight systems was a finite possibility, but they were effectively shouted down by the "you don't know what you're talking about - the hell with safety concerns" types.

The reason that some airlines prohibit in-flight electronics is that all the electronic environments under which they are used cannot be modeled accurately, so the ones that DO allow them are basically allowing time bombs having fuses of indeterminate length aboard their aircraft.