Been running plastic liners since 1987 in various trucks through the years and never had a rust problem paint chaffing yes but no rust. We had a 1993 GMC yard truck at work with a plastic liner and in 2016 they had it in the shop doing repairs now this truck was beat all to hell and back, they had the bed off and liner removed to access the bolts and not one spot of rust in that bed chaffing yes. On this truck I have a plastic liner and a rubber mat just to keep things from sliding around that don't need to be tied down.
My neighbor has a spray-in liner, he loaded it up with a bulk load of red mulch now his liner has red tint stains on it, looks terrible.