My rabbits are actually kept on laminate flooring over the top of my carpets to protect the floors. I'd recommend using cardboard pieces (mine love them to shred and for traction), and to add things like playmat interlocking grids as long as yours don't think they're good to eat. You may also be able to put down rugs as long as there isn't rubber they can get to and eat. Hope that helps some.
As with anything you put in their cage (rugs, playmats, etc) you should check to make sure they aren't eating it since a blockage is bad. Mine have adapted really well to wood floors and my one, Layla, even prefers running on wood floor. I think she likes to "rally slide" around things even if it freaks me out from time to time.