Only speaking domestically, state and federal prisoners are extradited from one state to another all the time. Often they fly commercial. There is nothing unusual about it. Also, there is a good chance that there is/are armed pax on any given flight you take, regardless of whether they are accompanying a prisoner. Just rest on that thought.

Prisoners are passengers just like you and me. If you have prejudice against flying with them, that's on you. Airlines are not obliged to rebook you, but they might do so as a goodwill gesture. And if you are curious to know what their offense is, cherish your right but be prepared to be told that it's none of your business.