I agree with everyone who is saying that the protectors do indeed protect the glass. They all work as advertised as I've used a protector for every single iDevice I've ever owned and have traded them all back to a Best Buy or an Amazon.com for top price. As somebody else said - it's protecting the backs from scratches that's a little more of the issue than the glass - though the glass DOES scratch much easier than is being characterized here in this thread. (my windshield of my car is riddled with scratches by way of example). It's true the glass is way more resistant to scratches than the plastic screens of the Treo days. But glass still scratches you have to turn it a certain way in the light to see the surface and the scratches. But those of you who don't use protection you might be surprised to see how many scratches are already on your glass.
I have ended up always using a case/folio for my iPads and therefore not using a protector for the back of my iPads anymore. But I still use one for the glass for the reasons others have mentioned - namely that I can't stand all the fingerprints on the bear glass and the shields (at least the Zagg InvisiShield) protect from oily fingers way better than the 'mythical' coating on the glass Apple says exists.
I will agree, however, that there is ever so slight a change in the way the retina display looks on my iPad 3 with my shield protector. Since I use a folio to keep my iPad in I will likely rip off the shield eventually to get back to "unprotected text" (love that - lol!). When you hand an iPad 3 to a Zagg vendor do they automatically install the HD version for you? I handed them back my screen protector that I had on my iPad 2 that I tore off before I traded it in and they gave me their 15$ warranty replacement (brand new one). Do you actually have to specify "HD" to them?