My GF asked for permission (on a TUI Transatlantic flight), not that she wanted to use it as a GPS but because it is a handheld PDA and she wanted to use it as such. CC said OK immediately, so I guess the airline staff vary in their knowledge of the subject.
Speaking as an engineer, I know that ANY receiver (well nearly any if you want to be pedantic, as there is a type that doesn't but they are REALLY rare), GPS, radio, whatever, has a circuit called a local oscillator which will emit radio frequency waves. The magnitude and type of these is such that they are almost certain NOT to interfere with any of the a/c systems, but many airline staff are not trained to make that sort of judgement and err on the side of caution (and I can't say that I blame them).
However mobile phones emit a much higher magnitude of radio frequency emissions - and it appears these can be used on aircraft!!
UFO