Trans[ortation from Venice, Florence, Rome to smaller towns

From Venice you can easily visit: Murano and Burano islands (via boat), Padua, Verona, Vicenza (via train).
From Florence you can easily visit most of Tuscany (via train or bus, depending on which town), like Pisa, Lucca, Siena, Arezzo, Pistoia, San Gimignano, Chianti, etc. You could also take a day trip to the Cinque Terre, although it's a 2.5 hour trip each way (via train).
The Cinque Terre is not the best as a base as there isn't much else to be visited nearby, so limit nights there to what you need strictly for the Cinque Terre (3 nights is more than adequate for most people, unless you are an avid hiker and/or scuba diver). From the Cinque Terre you can take an easy 1/2 day trip to Portofino (via train) or Portovenere (via train+bus, or a long hike).
From Rome you can visit Orvieto, Ostia Antica, Tivoli, the Colli Albani, etc.

Don't overlook Torcello while you are island-hopping in Venezia! Many convenient day trips from the cities you name, Roberto's list is quite good. I also like Frascati as a daytrip from Rome by train, as well as Castelgandolfo and Bolsena by bus..

Thanks. This is just what I needed to know. This is going to be such a great trip!!!!!

For easy-to-print train schedules for most of Italy and Europe, with timing and connections clearly listed, see the DB schedule link or mobile app. For buying tickets online or to see some trains from Milan to Lake Como, use www.trenitalia.com, but note that unreserved regional trains are not shown or sold more than a week ahead (better to buy those tickets in the station). Rick's guidebooks also summarize transportation from cities covered in the book to the next logical stops.