I think there is an issue to be made. While everything was legit, and the flight plan did get the necessary approvals, there should have been some better pre-publicity that CO's largest aircraft (and others, according to the NYTimes piece) would be making the low-flying patriotic landing into NYC.

With images of the 9/11 aircraft still fresh in the mind of NYC residents, and recent media about renewed threats to the region, the locals should have at least been alerted that a 777 would be lerking about rather than being surprised by its appearance.