I haven't got any scratches, and I have no cover. I keep my N900 in my right jeans pocket, but keep nothing in there with it. I also keep my screen wiper in my backpocket always, and if the screen is dirty I'll wipe it.

With proper use a normal user should never get scratches from the stylus.
[nerd]It's like a normal knife doesn't do anything to superman. You can stabstabstab, and nothing. Dip it in kryptonite, and it'll pierce :| [/nerd]