Always use a screen protector and if it is a good one, you will barely notice it is there. I have always loved the screen protectors from Screenguardz. Compared to the ones at Best Buy (forget which brand but they were stickier feeling), they are extremely smooth and the anti-glare is great. Here's their link...
[http://www.bodyguardz.com/screenguardzinfo|ScreenGuardz]
But, if you already have scratches in your touch screen since you didn't have a screen protector there in the first place ( duh, :D Just kidding), you might check out the different compounds from these guys. It looks like industrial grade stuff or something of the sort. Check it out here...
[http://www.tdillctechnology.com/resurfacing-compound-set.html|TDI-LLC Technology - Resurfacing Compounds]