Anything that touches the paint can cause light scratches/swirls. It's inevitable. Obviously, the more careful you are, the lower the chances, but the friction of another object rubbing the paint always carries the risk, however slight it may be.
Me, I don't use a cover. My garage is fine, relatively dust free, and I actually drive my car so it's already exposed to greater risk while driving, what good is a cover going to do?
'11 BMW E92 ///M3 - ZCP and DCT
'13 Toyota Tundra - 4x4 Platinum CrewMax, 5.7l iForce V8