We have used the metro system from the airport to Paolo's, stop at Octaviano, but you would have to do a change in lines, I think it was at Termini, and why I don't remember is because Paolo offered one time to book a pick up/drop off from the airport/his B&B, and that was it! Very convenient, reasonably priced, reliable, every time we have taken it, minimum of 4 times, always arrived on time and free of worries to Fuimicino. I would recommend to talk to Paolo about that service to the cruise port. Paolo is great at trying to help travellers, and he is very reasonable, then, a talk to him can take you a long way.
Have fun in your trip (I love Rome, and Italy! I wish I would be asking your questions ... That would have meant I was planning a trip to Italy, again :)