Here's what I did, both for our 4Runner and Subaru.
Stop by your local FredMeyer or similar and pick up a piece of
indoor/outdoor carpet in your fave color, 4ft width, and long enough to fit
entire stretch of back with seats folded down.

Cut it to length, and put it in the back.  Trim around the wheel-wells, etc.
Cut a slit for split fold-down.
Then, use a cover for the back like the Husky for supplemental and really
wet stuff.

My bike lives in my Subaru year-round, grimy and cruddy when doing club
rides in the winter.  I've never had the carpet underneath get remotely
dirty, using this method, over several cars.

Total cost about $20 for the carpet, plus the liner of your choice.

-pete