Just to clarify, use it as a loose guide for a decent route. Some of the morden route is designed for horse riding, on some stages between the old pilgrim stops the original pilgrim route is now a motorway!
I agree and in some ways it's the most scenic/interesting route. The main road from Empoli onwards is the Via Cassia and you can cycle on it - and probably if you use auto-routing software or route-planning software it's the one the software will suggest. It's the most direct option and at some points it's the most practical, but it's by a long way the dullest. My advice would be to avoid it where you can and in particular to climb to Radicofani (the traditional route) rather than taking the tunnel.
On the subject of tunnels, In case anyone gets the wrong impression from Brian's posts: the vast majority of tunnels in Italy (setting aside the open-sided ones and very short ones) are fully lit. I've cycled about 20,000 kms in northern, central and southern Italy and only come across one significant unlit tunnel (to the east of the Lago d'Iseo) which was pretty hellish but very much the exception. (Although I should say that I tend to avoid tunnels and roads with tunnels).
(Brian out of interest, where was this tunnel?).
Very few tunnels are off-limits to bikes (although a fair number of *roads* are off-limits).
Lights are of course a very very good idea.
If you take time to plan your route you should be able to cycle to/from Roma and encounter very, very few tunnels -if any. Indeed you could go from the border with Austria to almost Napoli without meeting a significant tunnel.
Coming through Liguria there's a tunnel in the coast (near a town whose name I can't remember for the moment) that you can't avoid, north of Lucca there's a tunnel that's off-limits to bikes, which you can avoid although there's no signposted alternative. If you're coming from the north-east there's a tunnel (possibly more than one) south of Bologna that you can avoid by going via the Lago di Suviana (following the Ciclopista del Sole bike route).
It's a good idea to get the Touring Club Italiano road maps (or Atlantide) and not rely on Google alone - the TCI maps have useful additional information - eg they show dual carriageways, which are often off-limits to bikes. They also show most tunnels. In particular, avoid if you can, any road with an E number. The OSM maps from velomaps.org are very useful (apart from anything else they show tunnels).