It's S.O.P.
Restraints are used for the protection of both the accused and the cops. It's the same way that the cuffs go on when you get a ride in the cop car.
This guy flipped out once, and he's a big guy, a 250-pounder according to what I read. It's a lot simpler to have him already restrained, compared to having to wrassle him down and hog-tie him, if he loses it under the stress of his circumstances. You could just imagine how people would react if he were to injure someone or be injured himself after an unrestrained outburst similar the one he had on the aircraft.
I used to transport Federal prisoners occasionally in a small aircraft. Those guys were thoroughly restrained, and dosed with a tranquilizer, plus it was two guards to one prisoner. It was nothing personal, believe me!