There is supposed to be a button to kick players out of ships (from outside the ship) if you are at a position where you can kick them (such as on planet, or docked in a ship they are on the crewlist for). That should be under Position->Travel if I am not mistaken.
If that is not the case, you may need to have an ASim move them manually. E-mail email@example.com with the details, especially ship ID.
I've got this problem too. I don't know if the faction has a ship with a tractor beam they can send down, but they directed me here first. Anyway, I've got no clue what the passenger's name is, or how to find out. When I try to kick him (or her, or it) I get "There is no docking bay" message.. or something along those lines.
If the ship is docked inside another ship, the passenger must be on the crew list of the larger ship for you to kick him into that ship. If you are on the surface of a planet you should be able to kick him without any trouble. You can't kick someone out into open space, if that is what you are trying to do, so you would either need to tractor it on board or NPC it with other ships of the same type to land it.