Enroute you are not using the GPS as your primary nav source. You are using it as another tool in your box. All information is required to be cross referenced to your primary nav kit ie vor's,NDB etc. And if there is a discrepency you go with the NDB,VOR's etc.
The systems that do allow you to use the FMC as primary nav source are because there is redundacy. And they have sitting in the background not only a GPS but also a VDU and which usually defaults to DME/DME fix's using 6 channels providing 2 fixes using 3 cross hatch distances. When they can't get 6 DMES they go to VOR/DME mode. If the GPS disagrees with the fix it goes with the VOR/DME data.
The idea that commercial traffic is going from A to B trusting only GPS to get you there is very far wide from the mark. And there are quite a few commercial crews out there that don't have a clue how to put a flight plan into the fitted GPS. They know how to use the direct button just or nearest and cycle through to get the point they want. FMC type machines are a bit different as the operation is included in the type rating. The machines that have been upgraded with a BRNAV gps alot of the old timers barely use it and its usually best if they don't touch it. I might add as well even without the wonders of gps they have no problems at all getting to intersections in the middle of nowhere.