We jumped a taxi (reasonable price)to the Spanish Steps which was the furthest point away from the station then worked our way back at a leisurely pace, stopping for food and drinks along the way, and finished at the Vatican which was close to the station. Rome is very easy to do on your own, you can choose where to see, and do it at your own pace avoiding the crowds as you go along. You can buy an excellent map of Rome for 1 Euro in most shops and plan your route for the day.
Villefranche has a few nice shops to browse through, with well priced Italian ladies clothes that are a little different. The tender to and from the ship was no problem, with no waiting either way.