I've done Rome on my own from the cruise port in Civitavecchia twice and find it quite easy, if you have done the research ahead of time. There is an all day train ticket from Civitavecchia to Rome and back with all metro and bus transportation included all day for 9 euros called the BIRG ticket. For more info, you can check out my site in my signature. I have a page on doing Rome on your own as well as a podcast devoted to the subject with a full itinerary Cruize Cast
You can also hire a private driver; there are many good companies, but they are comparatively very expensive.