I use an old Rhode Gear trunk rack. Various reasons that is the solution that works best for me. The rack has rubber mount points and rubber straps. I have a strip of soft fabric tied to each of the two mount points that wraps around the top tube, under the rubber strap. Thick fleece or flannel would work. I have some soft felt that came on a bike we unpacked and built at the LBS.
Also, I only use this rack for local trips. For long road trips I put the bike in the car. I don’t like the idea of the bike being sandblasted for hours on the interstate.