If you had ever disassembled a Honda seat you would have sean that, between the cover and the foam, there is a layer of PVC to keep the foam from absorbing water. I did it in my seat to paint the pan, and most of the PVD felt apart -it is heat-stitched with the cover to make the seat pattern-.
What I did was simply to use PVC from a discarded pool raft to make the isolation. Just make sure there are no bends that will mark through the seat.
Nevertheless, I bought at louis.de a waterproof seat cover for 5 bucks. It folds in a small package, and you can install it in a few seconds. Covers the seat completely, attaches from below with velcro tape. I carry it in the backpack everytime I ride and the wheather shows signs of rain.