If it is a very thin layer (or maybe made out of a special material), I would think a screen protector could work, but I'm not sure. On the other hand, by FAR the biggest cause of scratches on PDA/smartphone screens is the stylus itself. A little bit of grit or dust can get dragged by the stylus tip across the screen, making a scratch, or the tip of the stylus can get damaged when you drop it. We shouldn't have to worry about that kind of thing. However, we may have similar problems when using a cleaning cloth to wipe fingerprints off of the screen.
I do wonder what kind of cases there will be, though, since I don't think I'd feel comfortable just sticking a naked iPhone in my bag or pocket.