Instead of ship transportation I would propose to implement public transport paradigm, where you can travel w/o ship to somewhere. This is possible even while being offline. Ok, sometime I want to travel to my ship left somewhere far away. 
How I propose it to work:
Even players will be able to transport players.
If you chosen to travel somewhere by public transit - you will appear in the waiting room (if public transit is available to this point, if not - only by paying a lot to taxis).
Ticket on the bulletin board will appear to transport you somewhere. If nobody takes, then NPC will do the job.
And even if you are offline - you`ll continue travelling. If you log in to the game, but the trip is not finished you will appear on some space station waiting room (of course you can buy cheap Sidewinder and continue on your own) or whatever (if possible even inside the ship, looking in the window)
How I propose it to work:
Even players will be able to transport players.
If you chosen to travel somewhere by public transit - you will appear in the waiting room (if public transit is available to this point, if not - only by paying a lot to taxis).
Ticket on the bulletin board will appear to transport you somewhere. If nobody takes, then NPC will do the job.
And even if you are offline - you`ll continue travelling. If you log in to the game, but the trip is not finished you will appear on some space station waiting room (of course you can buy cheap Sidewinder and continue on your own) or whatever (if possible even inside the ship, looking in the window)