It's not because they can't, they know exactly what freqs and power output cell phones use. But to do the analysis for every aircraft type, for every possible avionics and antenna configuration, from every seat in the airplane would be very expensive.

Besides, they do interfere with comm, nav, and even aircraft systems. I've experienced all three. A certain type of cell phone (less common now days) if used from the rear of a CRJ 200 will set off the aft cargo smoke detector. Unfortunately, there's no way to access that compartment in flight to check for fire so it's a mandatory blow the bottles ($25K), divert to nearest suitable, dump the pax, and ferry home to get some more halon.

I also think airlines are reluctant to let the genie out of the bottle...they want the marketing boost from allowing premium travelers to what they do best (ie whatever the hell they want), but are afraid of what might happen when the inevitable confrontations ensue.