Hoh Humm,
this has been around for sometime now. Consider it a "gateway" type conspiracy as it is to suggest that the original passenger plane never actually hit the pentagon. So, the big question is where did it go?? Some theorists believe that when Cheney took command (while George was reading to children), he ordered that planes be shot out of the sky. I'm paraphrasing here, not real sure of the exact phrase Cheney supposedly used. And of course this begins the new conspiracy of: Did cheney order americans to be shot down because of the fear of more planes taking out institutions?
My opinion (not that I think anyone really cares) is that it is difficult to see the remnants of a Boeing plane on the Pentagon lawn or in it's walls, however, how incredibly difficult would be to cover this up?? My guess is it would be pretty frickin hard. So, like you, I find it interesting, and until someone comes up with hard proof, I must consider it a conspiracy theory.