We visited Rome for the first time last fall:
Taking the ship's tours from Civitavecchia is the only way to do it - because of the distance. The HAL Vatican tour is better than trying it on your own the first time for simple efficiency. We found Rome itself wonderful to walk in; we found a small laminated street map that kept us from getting lost - and every street and corner is a visual treat. If you can, add a few days and really enjoy Rome.