Hairline blemishes are usually in the coating on the glass, not the glass itself. (One MacRumors user went as far as to buff the coating off and in turn removed all scratches. Can't find the link to the thread right now.) If you can feel the scratches with your fingernail, they're in the actual glass.
Either way, all it takes is a single grain of sand to scratch a glass screen, even gorilla glass. If you are not particularly careful with the iPad, it will get scratched up. I would say start using a screen protector. It will hide the scratches and prevent further ones.
So I've got a TINY scratch on my new iPad, maybe between 5 and 10mm. Its small enough that it obviously isn't ruining the experience, but I can still SEE IT from time to time. I can feel it with my finger nail and it seems like it is magnifying the pixels a little (noticable on a lighter image), meaning that I see the blue, red, green, blue, red, green. I've got no idea where it came from as I am so carefull with it.
Would a screen protector hide that scratch too? If so, I'll go out and buy the ***** out of some screen protectors!