Our company does the same thing. We're charter, and on pax legs, F/O's are not allowed to fly. However, I can see why this is, because we generally hire pretty new low-time F/O's (about with the qualifications new regional airline FO's have), and most of the time, none of them have ever even seen a jet. FO's fly all empty legs, (at the discretion of the captain), and from the left seat. (We're in Citations). I see the reason for this policy, (at least at first), because almost every newbie may be able to fly, but they can't fly smooth. They also have the tendency to get waaaaay behind the airplane (yes, even in a Citation), and that is simply a product of never being in a jet before. I know I was that way when I first started, and I learned a LOT simply from watching experienced captains fly. Corporate is a lot different from airlines. If you have a new FO flying the plane, and slam some rich guy all over the place, guess what, he's taking his money elsewhere. In the airlines, you go up front, slam the door, and if you give the pax a rough ride, what're they going to do? Nothing. Once the FO proves that they can fly the airplane smoothly and stay ahead of it, then they can fly pax legs. You get a guy with previous jet time, they're good to go almost right off the bat.....it's just learning the nuances of a new airplane. Stick a guy in there straight out of a 172, and chances are he'll be so far behind the airplane he'll have to rent a car and drive to our destination after we get there.
On my flights, the FO gets all empty legs in the left seat if he wants 'em, with a few exceptions. Examples would be putting a brand new guy in bad weather, or making someone land on a short narrow runway when I'd never seen them do it before. Usually, after someone gets some time, and they're flying, we'll be going home to our 8000 foot runway, and I'll say something like, 'OK, pretend like this runway is 75 feet wide and 3800 feet long. That's all you've got.', or 'OK, your autopilot and flight director just died, and you have to shoot an ILS down to mins.' If they handle it with no problem, then I know that I can let them go into a short runway in the left seat, or fly in bad weather to an unfamiliar airport.