I've become wary of foam-type cushions - I had some foam covered tool hangers from Home Depot I used for guitars which did a good job of messing up lacquer finishes after very brief contact.
No rubber pads, yet. I'm thinking of using adhesive felt strips instead. The type which are used to prevent table legs from marring wooden floors.
The wood used for the stand is spruce and quite soft so I doubt it will damage the guitars.