Personally, I prefer to use the public transport when I can - especially the trains. The type of public transport however will depend mainly on where you will be based and what you want to see, for example Florence - even Pisa - can use the trains quite easily to get around.
But many places can only be reached by bus for example San Gimignano. And even then, many buses do not go from the top to the bottom of Tuscany, they are divided into ares - those that are around Florence or Siena or even Lucca and Pisa.
Here are a few links that should help you sort things a bit, and if you want to let me know where you are staying then I can try and be more precise.