I wonder if it might have something to do with the material/dye?
I've used fender covers from this company for years and have been very happy with them:
Procover Boat Fender Covers
I use the dark green and the color has NEVER rubbed off on my hull. Nor, have I observed them causing any wear on the hull. In fact, the main reason I started using them years ago was to reduce tiny scratches "clouding" the hull at each location where the vinyl fender was continually coming in contact with the hull.
I wash the fender covers once or twice a season in a washing machine. When doing canal/lock work, I rinse them off rather frequently - most often by simply dragging them in the water a bit while under way.
I replace the covers every 2-3 years because they do tend to fade a bit and get somewhat loose. They're inexpensive enough, so I don't view this as a problem.