Hmm, seems to me that airplane design needs an overhaul for the electronics age.
A few crazy ideas, just for the fun of it (I know absolutely nothing about aircraft design):
1) passenger cabins should really be encased in a Faraday cage, though that will degrade the view from the windows
2) mount GPS and other vulnerable antennae on wingtips, to reduce signal strength
3) Add more GPS satellites, boosting signal strength and allowing for a reduction in the sensitivity of receiver antennae