in 20 years of hauling rafts around on mostly unfinished wood decks I've never had a splinter be an issue... and in fact, feel that if a splinter damaged my boat I'd seriously reconsider trusting the boat on the water.... I mean rivers are filled with pungy sticks, sharp rocks, occasionally even fence posts; all kinds of things that are much tougher and scarier than a splinter...
With that said, I added 12" HDPE runners under my tubes a few years ago and love them. They are there to reduce friction, not protect the boat but they do add a layer of protection from those pesky splinters as well.
I highly recommend this concept! Plus you can make the center of the trailer grippy to aid in loading or keep you from sliding off the trailer on a steep ramp (BTDT...)