I've stayed in several Ryokan's in Kyoto and Hakone. If the place you stay is a quality inn, then I'd lay odd's that you'll have one of the best night's sleep you've had in a long while. Futon's are extremely comfortable when everything is well prepared.

I'd say go for the experience. Take off your shoes and put on the slippers (don't forget to change slippers when in the bathroom) and the yakuta, soak yourself for an hour in the Onsen, enjoy a decadent meal in your room, take a walk and when you return your futon will be waiting.