We did exactly this last year! With only a few hours in Rome they will definitely be limited.
We chose the "Rome on Your Own" tour from the cruise, which was a bus ride to and from the city. Dropped off at the St Peter's. Did an unguided tour of the basilica, bought the HOHO tickets at the end of the piazza and away we went.
We'd been to Rome for a numbers of days before, but were with another couple that hadn't been, but they did want to see as much as possible. This did not allow time standing in line ups for museums or the Colosseum.
We stayed on the bus and rather enjoyed the audio tour all the way to Piazza Venezia. We got off there and walked to Piazza Navona (for lunch), then the Pantheon and then to the Trevi Fountain. Ended up taking a cab back to St Peter's to catch the bus back to the ship.
This is an OK way to get a good overview of Rome and "see" the main tourist attractions in a very short period of time.
I hope this isn't going to be their only trip to Rome because you truly cannot appreciate all it has to offer this way, but that said I think it's better than not seeing it at all.
Had it just been my husband and I, we likely would have taken one of the other tours or hopped on the train to elsewhere from Civitivecchia.
Linda