Good question. Ford apparently doesn't like it much. On page 405 of the 2011 F-150 Owners Guide (1st Printing) you will find the following warning:
Note: Failure to use the correct air filter element may result in severe engine damage. The customer warranty may be void for any damage to the engine if the correct air filter element is not used.
Okay, what does that mean? What is a "correct air filter?" Does that mean that if you have a Fram or Purolator air filter (indeed, anything that doesn't have a Ford or Motorcraft part number) in the factory air box, your warranty is void? No. In fact, K&N will go to war with you if any factory voids your warranty because you have one of their filters in it.
Here's another question: Does that warrning in the Owner's Guide mean that ANY engine failure will be attributed to the air filter if you have what they consider to be an air filter that is not "correct?" Very unlikely. If you blew a coolant hose or if the crankcase drain plug popped out, they'd be pretty hard pressed to claim that the resulting engine failure had anything to do with air filtration.
So what's it mean? I'm not sure myself. I've read that there is a federal statute that limits manufacturers' avenues for voiding warranties, but I've not read the law myself. I have also read that a great deal depends on how the dealership in question views modifications. And that, of course, varies all over the map.
Anybody with some first-hand experience with this particular issue? I bet there are few or none. I don't know what an engine failure due to air filtration would look like or how it could be proven.