its amixed message really, you have to choose your priorites. I've had a couple and they do impart scratches on the soft plastic of the windows. However, these do polish out with a bit of work. the alternative is to leave all your plastic panels and, possibily more importantly, all those mastic joints exposed to rain, wind and UV.
A cover has many faults, but personally I found it a great comfort to know that that melting layer of snow on the roof couldn't seep into any failing mastic joints. (even an optomistic mastic manufacturer would have to admit it has a short life span when exposed to the elements) Also the van stays clean and doesn't fade in the sunlight, meaning it looks much better tan other vans when you come to sell it after 10 years. I've only ever had the tailor made ones though, and even they flap about in the wind, increasing scratching - don't think I'd go for a baggy multipurpose one.