If you plan to visit just those 3 cities then the only logical thing to do is connect them by train. You can't drive to sights in the cities - there's no driving from your hotel and parking at the Colosseum, for example. You would need to park the van in a garage outside the city, then go to your hotel, and walk or take transit/taxis to the sights in the city. If you found a hotel with parking it would likely be far away from the city center, necessitating taking long cab or bus rides into the city, which doesn't make a lot of sense as you would be limiting the time seeing what you came to see - and it makes it very hard to enjoy early mornings or late evenings in the city, which is the best time (less crowded, better light for photographs, great atmosphere and lighting for after dinner walks).
A van could be useful if you want to explore the countryside, but then you'd probably want to rent it when leaving one city, spend several days exploring the region of your choice, then return it when arriving in the next city. Tuscany is a popular place for this type of exploration, so renting a car after Rome, spending time in Umbria and Tuscany, then returning the car in Florence area is a reasonable plan. Do note that many small towns also do not allow you to drive into them - there are parking areas on the outskirts and then you walk or bus into town. Also, small towns have train connections, too - so you don't need a car for a simple day trip from florence to a tuscan town - more useful for connecting several towns and visiting rural parks/wineries/etc.