Phones, computers, even radios have oscillators in them which radiate in the RF band. Multiple oscillators reflecting off the inside of a metal tube could potentially cause unpredictable interactions with the plane's avionics. Probably won't, but why take the risk? Losing communications for a short time isn't worth making a hole somewhere.
Then, too, they may have other concerns. Would they consider a phone or computer to be a remote triggering device? It's possible, but the prohibitions predated 9-11.