I was like, ‘Dude, personal flying armor, Norse gods and alien invasion!’ but apparently it’s something else. They did cooperate fighting Decepticons.
The Pentagon didn’t like that it was unclear to whom SHIELD answered. Was it to the UN? the US government? It was never certain (even in the comics) so they just shook Marvel’s hand and walked away. Although someone commented that SPOILER ALERT Nick Fury disobeyed the order to nuke New York.
More on Wired: http://www.wired.com/dangerroom/2012/05/avengers-military