Italy in 2 weeks in September

It's almost impossible to get to the small villages and towns of Tuscany without a rental car. If you are more interested in culture and touristy sites you should consider renting a car.

Donna

Not a lot to sink ones teeth into with your post.
I am thinking that Milan would be the best airport to fly to as there are direct flights from North America. Florence would mean flying to a European gateway and changing there.
You could make it a circle trip either clockwise or counter clockwise. I am thinking clockwise and take train from MXP to Parma via Milano Centrale. Recover from jetlag in Parma and see a few sights there. Then take a train to Bologna, stopping in Modena on the way for a few hours before proceeding to Bologna. stay there for 2 nights to give you a full day there. Head to Florence next morning and camp out for the meat of your stay. You can visit Siena, Lucca, and Tuscan hill towns by bus or train from Florence. Last part, head to Cinque Terra for 3 nights. Then train to Milan via Genoa. Over night near Milano Centrale and see a few things that afternoon and evening. Early train or bus from Milano Centrale to MXP for flight home.

I agree with Donna - you'll miss lots with no car but the so called tourist traps like Siena, Florence, Rome, Venice, etc. are magnificent and you sure don't need a car from those.

You could also fly in/out of Pisa, which is a larger airport than Florence, so you may have more options. It is closer to Cinque Terre and you could visit Lucca, which is a medieval walled town.

Some friends of ours wanted to spend some time in Northern Italy before they joined a Rick Steves tour. They flew into Milan and then took a train up near the Lake Como area and then had a private driver take them on a tour. They are not rich people so this was not unreasonable to do for the average person.

We are planning a trip to Italy in September too. I'll just mention our trip after we complete the RS Southern Italy tour:
1) Florence hotel for 7 nights - this will include day trips to Pisa (train) and also Siena (bus). Will use the Firenze pass for 3 of these days (see RS book on pass).
2) train to Assisi for 4 nights - in addition to Assisi will use bus and train to visit Perugia, Spoleto, and maybe Spello. See the Fodors 2015 for these towns outside of Assisi
3) train to Rome - we will just finish Rome up for 2 nights having done a few nights earlier. Rome flights give us the best connections to return home.

We have specifically avoided too many hotel checkin-checkout's as this can be tiring and take up valuable time. We did not include Cinque Terre on this trip but the Southern Italy trip has a coastal town in it.