I have aluminum - it came with wood bunks covered with carpet. I soon noticed corrosion on the hull where it rests on the bunks. The carpet holds salt water against the aluminum - perfect conditions for corrosion.
The carpet also holds water against the wood. If the wood cannot dry out, it will break down more quickly.
I removed the carpet and the wood was starting to rot. I replaced the bunks with new D.Fir (higher grade for strength) and attached a layer of polypropyline plastic (not sure of spelling - this is what is used for cutting boards) on the upper surface.
That was 2 years ago. So far - so good. The boat slides very easily - both at launching and loading. (In fact, you have to be careful not to have too much speed when running the boat onto the trailer, the plastic is much more slippery than the carpet).
I haven't noticed any worsening of the corrosion. The plastic does not damage the aluminum. The wood is still in perfect condition.
I chose untreated Doug Fir because it is a lot stronger than cedar and the trailer is dry most of the time. If you keep your trailer outdoors, i would recommend cedar or pressure-treated fir.
Glass boats are a different story - would the plastic surface harm the glass hull?