There's an interesting (and funny) blog post by Evan Butterfield about his experiences with his Kindle and an iPad. He complains that the iPad he played was quickly covered with fingerprints, smears and smudges. His Kindle doesn't suffer from those (nor does mine).
I have talked with Sriram Peruvemba from E Ink, and he said that E Ink indeed offers a coating that is anti-fingerprint/smudge resistant. This protective coating is designed and supplied by E Ink themselves as an option to their customers. This coating goes on top of the E Ink Vizplex or Pearl imaging film, in the form of a protective layer.