With the internet on domestic flights, I wouldn't be surprised if we see tweet pics of him on the plane.
They have special transport for inmates. They don't sit shackled inmates in with regular travelers. Too risky and dangerous.
In the movies, criminals are transported in 10-car convoys with decoys, helicopter escorts, and an army of well-coiffed agents in black suits. (Somehow the prisoner still manages to escape and uncover the real culprit and clear his name!) Given the size of the US prison population—at almost 2...
The US Marshals Service  operates the biggest prison transport network  in the world, called JPATS (Justice Prisoner and Alien Transportation System), headquartered in Kansas City, Missouri. JPATS has its own fleet of 10 planes, ranging from a six-person Beechcraft 99 to an MD-80 that can carry about 140 inmates  . (Yes, it's nicknamed Con Air.)
Remand of Custody
When custody changes hands, prisoners get a pat-down  . For airport transfers, a shotgun-toting  tactical team from the Bureau of Prisons is on hand. Someone is also there to oversee the paperwork . (This includes medical records: If a prisoner doesn't have their proper meds, they don't get to board.)
Security in the Sky
The flight  our photographer was on had as many as 15 guards. They spell each other every 15 minutes, eyeing prisoners from the front, middle, and back of the plane. Firearms are generally a very bad idea in pressurized cabins; that's probably why our photographer never saw guards in the air armed with anything other than Tasers .
Inmates travel in cuffs, shackles, and a belly chain. More dangerous customers are fitted with a "black box " , a plastic casing over the chain linking the handcuffs, to further hamper movement. Lavatory visits require the company of a guard  , and the door remains open at all times. (Mental note: Never complain again about the indignities of flying coach.)
There's no in-flight movie, and no one is allowed magazines or books of sudoku puzzles. Meals  are decidedly no-frills affairs. Sample menu: corn chips, turkey bologna and cheese sandwich, cookie, and water. Tray tables have been removed from the seats to preclude enterprising inmates from weaponizing them.
Re-remand of Custody
Prisoners can be marked to denote destinations. (In this case, an X on the hand  may mean that he is to be transferred to a particular jail.) Nick Cage notwithstanding, the JPATS says it has never had an escape, and that airborne violence is rare. (All in all, better than your typical flight out of LaGuardia.)