I have a cover and I think that if you are careful about it there is nowt wrong with using one - and this is from a person who spent £220 on a detailer to come out and remove swell marks from a new 06 car!
For example, I washed it the weekend before last and stuck the cover on it (I have a four layer 'Stormforce' all weather cover from Cover-Zone - cost me £120), I did not use the car again 'till this Sunday. Once the car is used from clean dont put the cover on again until you have given it a good clean again, and be careful when you put on and remove the cover - roll on, roll off - you'll know what I mean if you get one!
G