If you believe Eric Johnson's opinion about the back cover on his strat, that will surely kill your tone!Get a Scratch Pad! I never thought I'd get one....but it's great.
It's doesn't cover 100% of the guitar, but enough so there's no belt rash. You might get some marks towards the bottom of the guitar due to those metal things on your jeans. But the only way to 100% protect your guitar is to play naked.
It's also nice because it keeps your guitar in place while you play.