If you follow the advice to go to Lake Como take the bus from the Malpensa airport or take the train (transfering in Sorono(sp?)). You don't need a car at Lake Como--you will be using ferries and water taxis. So, you will pay for the car, pay for the gas, pay to park it at the outskirts of your town, and probably won't use it. Ditto for advice to go to CT-- towns are car-free.
I want to echo what others have advised: take the train from Milan to Florence instead of incuring huge fines by driving. You will have to park outside of the city center so once again you're paying for a car, parking, risking traffic fines, possible vandalism and you can't use it in Florence.
It's a 45 minute bus ride from Florence to Siena (by the way Siena city center is completely car-free.) I also found driving near Siena is confusing. Additionally, parking can be expensive and hard to find. After a stressful, time-consuming search, you may end up parking quite a distance from the city center. Take the bus.
Search for "traffic tickets" to read the sad, sad stories of people who drove when they shouldn't have.
Also, prepare yourself that no matter how much research and preparation you undertake you may still receive a ticket in the mail many months after you come home. That's part of the cost of driving in Italy.