Ever since I started using a Wish Blissey with Protect, I've become very fond of it. It's particularly helpful when out against obvious Choice Item Pokemon - like CB Garchomp, or ScarfCross/CBCross. It lets you scout the moves. For example, I run a Skarmory and a Spiritomb on my teams. Skarmory takes a bit too much damage from Heracross with Close Combat, and Spiritomb takes a bit too much damage from Megahorn. If you use Protect, you can find out which move is being used, in turn giving you the advantage and not worrying about sending out the wrong Pokemon, or perhaps being out-predicted. If the Heracross uses Close Combat, he'll say hello to Spiritomb, or a Ghost type - likewise, if he uses Megahorn, Skarmory will pop up. So in that case, it tends to be extremely useful, if your team has a particular thorn, a Pokemon with Protect could put you at an advantage.
Oh, and it also gives you a free turn of Leftovers recovery.