Flannel lined cotton covers are old technology nowadays. They allow dust to pass through the cover, since the weave is open, and the cotton absorbs moisture that's in the air. A much better choice is Dustop, which a material Kimberly Clark makes. It will block dust, and doesn't absorb moisture.
I have Evolution 4 and Dustop covers for all my cars, and they get used every day. I have no problems with them marring the paint surface, but I take the usual precautions:
1) wash and dry
2) California Duster
3) Quick Detail
before putting the covers on. Even on my airport car, I dust them, and quick detail before slapping the cover, cable and lock on, and after 5 years the ol' Contour SVT looks great.