In the US, federal air regulations are administrative law, not under criminal law. Therefore flying a plane without a liscense will not automaticly get you thrown in jail. The FAA has no power to arrest anyone.
However, the local district attorney may be able to make some local or state charge fit, like reckless operation of a motor vehicle or something. When two airline pilots tried to fly drunkout of MIA, the local DA charged them with DUI. Since the florida law does not specify what type of motor vehicle, he tried to make it stick. I can't recall if it got overturned or not.
In extreamly rare circumstances of extreame negliance resulting in a fatal crash, some people have been charged with manuslaughter (I read of one conviction). The maintence supervisors who cut corners storing O2 generators that caused the ValuJet crash were charged with manslaughter.
Customs and TSA regulations, DO fall under criminal law and you CAN be arrested by these federal officers or local law enforcement.
Regardless of all this, rember the golden rule of dealing with Police in America. They have a gun, and if they take you into custody, and you resist you are going to face a new set of charges or worse.