A dry sack is ideal. I have one just like the fellow who has the yellow Nelson Riggs one for sale. It is designed for kayaking I believe, hence guaranteed waterproof and not too big so it can fit on the rack. In my case I put it on the passenger seat and put my bike cover on my trunk rack as I don't want to put too much weight on the rack/trunk lid and stress out the mounting points.
As a footnote, I put clear plastic tubing inside the weather seal around the top lid of the trunk (the black weather seal is hollow). This provides added strength and helps prevent and stop the top lid grinding down on the trunk base and leading to stress in the plastic and wearing away the paint, etc. To insert it easily I sprayed it with silicone lube into the existing weather seal. Then I removed the sharp edge at the end of the tube and made it tapered so that it would be able to easily push it all the way around the weather seal at the corners where it could get stuck. Take your time and massage the weather seal and it will go. Now your seal is much stronger for the trunk lid to rest on!