I will be using the trains from Rome to Florence, to Cinque Terra, and over to Venice. Can I get on and off the trains to visit small towns and is this easy traveling by train?
If you're traveling by regional trains; i.e. ones that don't require seat reservations, then yes. The "small towns" you would see are ones along the train routes, of course, and that the trains stop at. Do you have specific places in mind?
Most trains that run from Rome to Florence are high-speeds with many of those being non-stops. You will not be able to hop off/hop on the high-speeds. The Regionale-class trains are a different story. The Regionale ticket is an open ticket from point A to point B. In this case, we'll assume Rome to Florence. This open ticket is good for 60 days and you can jump on any Regionale train making this run. BUT, as soon as you validate your ticket, you have 6.0hrs to complete your journey. But, you could hop off/hop on at Orvieto, Chiusi, Arezzo and other towns on that leg.
For your journey to the CT from Florence, you will most likely be on Regionale trains although there are some runs with ICPlus trains that do require a seat reservation. Most runs will require a train change at Pisa or La Spezia Centrale or on some runs, both. Many travelers do take the opportunity to hop off/hop on at Pisa to see the leaning tower. The Pisa train station does have staffed luggage storage.