Two days are not enough for the Naples area (Amalfi Coast, Sorrento Coast, Capri, Pompeii, etc).
However two days are good enough for the Cinque Terre. Since you already plan to be in Tuscany and the Cinque Terre are in Eastern Liguria basically at the border with Tuscany, it makes sense to go there.
If you plan to rent a car while visiting Tuscany (which is a better idea to maximize the number of small towns and countryside you can see), you should drive to La Spezia, north of Pisa, and return your car in La Spezia. Then take a taxi from the rental drop off location to La Spezia Central station and proceed by train to the Cinque Terre (a car is a useless and expensive hassle at the Cinque Terre. When you are done with the Cinque Terre, take a train to Rome from there. You will likely need to change trains in La Spezia (unless you stay in Monterosso). From La Spezia to Rome there are several direct (no train change) trains traveling along the coastal route, that will get you to Rome in 3.5 hours.
If you don't rent a car in Tuscany and stay, I presume, in Florence, then take a train from Florence To the Cinque Terre. Likely 3 Train changes from Florence to Cinque Terre (at Pisa and La Spezia).
