Sounds like he mis-spoke. He was referring to the terrorists shooting down the plane. It sounds like he meant to say they brought the plane down, not shot it down.
Plus there's plenty of 911 evidence (meaing the number 911, which was dialed by a few on the plane), and evidence from other recordings, which indicates that the plane wasn't shot down, but was crashed by the terrorists.
Rumsfeld's quote is this:
"I think all of us have a sense if we imagine the kind of world we would face if the people who bombed the mess hall in Mosul, or the people who did the bombing in Spain, or the people who attacked the United States in New York, shot down the plane over Pennsylvania and attacked the Pentagon, the people who cut off peoples' heads on television to intimidate, to frighten indeed the word 'terrorized' is just that. Its purpose is to terrorize, to alter behavior, to make people be something other than that which they want to be."
He said the "people who attacked the United States in New York, shot down the plane over Pennsylvania". That isn't referring to plane being shot down by the U.S. military.