I'm assuming your looking to keep crap from getting trapped and causeing rust, best solutions I've seen is to coat the inside of the rockers w/ bedliner/undercoating to give it the rubberized effect, can also do the tube where the rockers cover. I've also seen people use caulking, just make sure to get the stuff that stays flexiable, and run bead around the outer edges to seal it up.
If you run a sheet of rubber there is still a good chance of getting crap caught between the rubber and the tub.