Absolutely, there are a whole range of protective covers and you'll find a wide discussion on the Forum about the pros and cons of the various types.
A friend of mine had a similar problem with a scratch on another touch screen device (not an iPad, though) and, before fitting the protective cover, wiped a *very* small quantity of petroleum jelly ('Vaseline') over/into the scratch. When the cover was fitted, the scratch was completely invisible.
Tim
Scotland