Angela,
Would you mind sharing your finalized itinerary? That would help us provide better information. For instance, are you still flying in and out of Rome?
We rented from Hertz at FCO and didn't have any problems. I'm a Hertz Gold member and rent frequently for work, which might have helped.
IIRC, you are traveling with a fairly large family group. I'd weigh the expense of train tickets for the rest of the trip against your suggested drop off locations. It may end up that the daily rental cost is close to the cost of public transportation.
Finally be aware that Ken copies and pastes the same scare stories any time someone mentions renting a car in Italy. Our rental experience couldn't have been more different, we had a wonderful time driving around Tuscany. If you use the internet to familiarize yourself with the basic rules and signage, you should have no problems navigating Tuscany in a rental car. We chose to avoid driving in Rome and Florence, but had no problems finding parking and keeping out of the ZTL's in Siena. Everywhere else ZTL's are clearly marked. As a rule of thumb assume that if the city has a wall (Radda, San Gimignano, Volterra, Siena) that anywhere inside the wall is ZTL. Also, speed limits are clearly marked and easily observed. Remember that they use automated speed control systems and just because you don't see a police car (we almost never did), that doesn't mean your speed is not being monitored.