I would think that a lot of it will depend on the material the cover is made of.
I drive my car to work pretty much every day its not raining, and I cover it every day that its not excessively windy with a cover I bought 8 or 9 years ago from North Coast Tarpaulin Works in San Diego (they've evidently changed their name to "Coast Car Covers" at
http://www.coastcarcovers.com ). I forget the exact material mine is made of, but its fairly thick, and textured - looks like it could be the "Evolution 4" or "Noah" fabrics - is highly water resistant, and has a flannel-type material on the inside.
My car is black, and thus its fairly easy to see any paint problem, scratch, etc. Even though the cover is an exact fit for my RT/10 (with or without a top on, it fits extremely well), windy days will cause the cover to flap against the car and create rub marks where ever there is a seam in the cover, hence my qualification about not using it when windy. I used a silicon-impregnated duster on the paint quite often (e.g. a California Car Duster or generic similar one), but I've never had a problem with existing dirt/dust scratching the paint. More of a concern is getting the inside of the cover dirty - as, if you do get the inside of the cover dirty/dusty, it will tend to transfer back to the car when the car was otherwise clean.
Condensation-caused dust, etc, has not caused any problem with the cover or paint in my situation, although it may not look that good after you take it off as you'll see mottled spots of dust and such on it, but it won't cause any damage. Maguires Quick Detail will make short work of any condensation-attracted dust, or, in fact, most any other problem short of actual dirt clods stuck to the paint.
