Less Common Now
It is less common now to see a prisoner transported on a commercial airline because the U.S. Marshalls service is using its own transportation network which includes planes, and state and local law enforcement agencies have developed their own transportation nets.
Part of my law enforcement career was spent as a deputy sheriff. My gripe was when returning back home without a prisoner a law enforcement officer had to check his/her sidearm in baggage, and they put a BIG RED TAG on the hard sided bag (it had to be hard sided). The tag announced to the world that the bag contained a firearm and all but announced to the world to STEAL THIS BAG.