I see your point, and I'm not suggesting that AF1 just goes and does whatever it wants. But, certainly, if they want to take off they can; and certainly, they're not following the same sets of procedures and protocols as the rest of us. That's my primary point here.
Also, I'm fairly certain their flight plan is ambiguous to say the least. On multiple occasions, we've been grounded because the Pres was coming somewhere nearby. But, he never came or was never any where near us. Now, maybe he changed his plans. Maybe they file several false plans to make scheming more difficult. Maybe the FAA just didn't want us in the air. One thing is certain, I'd be willing to bet someone from the Secret Service is reading this thread right now with all these references to AF1 in here.