The police department said it had been notified about the flight, which involved a pass over the Statue of Liberty, but said it had been barred by the FAA from alerting the public.
They do this to protect the Most Important Human Being in the Universe. Can't let the hoi-polloi know where their Master will be, as they're afraid someone will make
use of that information.
Now, if they panic a bunch of folks (probably hurting more than a few... can you say "heart attack"?), it's ok. Just so long as the Chosen One is protected (even if he isn't really on the plane). They really figured they needed the photo op more than the common folk needed their safety and feeling of security.
Woulda been interestingly ironic if they'd had a problem and ended up crashing the blue-and-white whale into a building in NYC.
(added): we private aviators are required by law to operate at an altitude sufficient to allow for a safe glide to a landing spot in case of emergency, or at least to avoid endangering any persons or property on the ground. A 747 at the reported altitude probably would not meet that requirement. However, since they make the rules, they don't really have to follow 'em.