I Had the same problem, So i got a peice of plywood and cut it to the exact shape of the tray and put marine carpet on it. It came up a million bucks, whats also great is you can just lift it out when you want to put a dirty or heavy load in.
Heres a few pics:




As you can also see in the pic my tray is only in primer from when i panted my hardcover,but i plan to paint it with a product called "pannelfleck" its a ute lining paint. ill post some pics when its done (maybe after christmas at this rate.......)
Hope this has been some assistance.