How do you plan to use the bed?
No matter what you answer, I would dump the plastic liner. If for no other reason that it does kill the paint underneath (as has already been mentioned) whether your using it or not.
If you plan to hard use your bed, then LineX all the way for sure. IMHO nothing beats it when it comes to work truck type applications; hauling gravel, wood, steel, chemicals, dirt, etc etc etc...
On the other hand, if you don't plan to haul that heavy duty kind of stuff all the time, and instead want to use your truck for occasional work stuffs, as well as haul crap like a TV or furniture or whatever else has a finish you care about, IMHO nothing beats a BedRug.
I've had LineX on my personal trucks in the past (not the Raptor) and we have it on our work trucks and it flat rocks. Seriously, other than fading over time due sun exposure, there was nothing I could do to the stuff to hurt it.
But I don't tend to use the Raptor for the seriously dirty/hard use stuff, and I do tend to use it for stuff like hauling groceries, household crap, camping gear... and for that the BedRug is by far the best solution. Where the LineX is super abrasive, the BedRug is, well, rug. It grips the stuff really well, and it doesn't mar any surfaces or wear holes in any fabrics or scratch up whatever.
And in a pinch the BedRug can haul the nasty stuff too. It just takes a while to clean up after (lots of high pressure water).
So, yeah, how do you plan to use the Raptor? The answer to that will probably also answer your original question. Hope that helps!