My safe shelves are upholstered but the best thing I have seen used is the tool box drawer liner. It's padded and oil/chemical resistant material sold in rolls to cut to size.

 

Mine are covered with a felt material, but I like the tool box liner idea.

 

I've dealt with the problem in a different way. I place handguns I am more likely to use in either a pistol rack inside my safe (similar to this one - HySkore 6 Gun Modular Pistol Rack Closed Cell High Density Foam Black) or in magnetic gun racks like this one that I place on the inside walls of my safe --- Benchmaster Pistol Rack 1-Gun Magnetic Strip Closed Cell High Density. These work great, but my safe has no carpet on the inside of the walls, which helps. And I can't use these for heavy guns like a SW N-Frame revolver.

I place my other handguns in pistol socks with tags to identify them or, in some cases, keep them inside the original manufacturer's box. My safe is old and ugly as sin, but it literally weighs more than a ton empty.

 

Another vote for racks. I use the Hydcore foam racks which also gains you some real estate back if guns have laying on their sides. A couple go into the pockets on the organizer on the inside of the safe door