Transportation from Rome to Sicily

We used AirOne (Lufthansa code share) from Rome to Palermo. Short flight, so more time in Sicily. Bags checked all the way through. Palermo airport TINY! Way back to the mainland, we took the overnight ferry to Naples, as we spent 3 nights in Sorrento exploring the Amalfi coast. Train is a LONG trip. Why waste time sitting on the train when you can be in Sicily within a few hour via air? Good luck with your travel planning!

There is a direct IC train that leaves Roma Termini at 11:39 and arrives at Messina Centrale at 19:30. It makes other stops beyond Messina and goes as far as Siracusa. See the timetables on either trenitalia.com or bahn.de. If your plane arrives on time at FCO, you should be able to catch the 10:38 Leonardo Express train which leaves the airport at 10:38 and arrives at Termini at 11:10, giving you time to catch the 11:39 train to Sicily.

If you found a flight to FCO it means you are flying either AirFrance AF 4328 or AF4330 departing at 7:10 or 19:25 respectively. They are the only 2 flights from MRS to FCO. Both are a code share with Alitalia. They arrive at FCO at 8:30 and 20:45 respectively.
So why not purchase a ticket all the way to Catania CTA (via FCO)? There are Alitalia (Airfrance codeshare) from FCO to CTA six times daily, 5 of them available for your arrival time from MRS. Alternatively, instead of Catania, you could fly from FCO to Palermo (PMO) still with Alitalia (AF codeshare). Alitalia has 6 daily flights to PMO also. A train from Rome to Sicily is a long long journey that never ends (8 hrs to ME only). Why would you want to do that to yourself? The difference in price with AirFrance/Alitalia is probably not significantly higher to fly MRS-FCO-CTA (or PMO) than to fly only to FCO and then take the train. You'll be in CTA or PMO in one hour and you don't even need to pick up your luggage at the carousel till you get to Sicily and no need to transfer from FCO to the Termini station.

The flights you mention from MRS are $770 to PMO & CTA. The flight from MRS to FCO is only $77.
An extra $700 each for the trip down the coast seems steep!

If you really want a train, go to trenitalia.com for fares and schedules. Personally I would fly, perhaps from Genoa (closer to france) or Milan, or even Rome. Trains from Rome to Catania take 9 hours, from Rome to Palermo 11 hours (Roberto gave you the info on Rome to Messina). There are overnight or daytime trains. This is a long trip and delays are not infrequent (it took 13 hours from Messina to Rome in 2011).

You can fly non-stop from FCO to Catania on Air Italy for less than $100 US. You can fly from FCO to Catania (one connection in Sigonella) on Meridiana for less than $100 US. See skyscanner.com for timetables.

Check Nice (NCE) too. I just searched some flights from MRS/NCE to CTA/PMO on Kayak for a sample week of Jan 9 to Jan 16 and found plenty of flights with Alitalia for less than $300, with one stop (either FCO or MXP) I don't know the dates you need to travel but if you go to Kayak.com and enter in the fields the airport codes separated by a comma FROM: MRS, NCE and TO: PMO, CTA you should be able to find flights at a reasonable price, probably comparable to a plane+train combination. Also, in addition to the major airlines, such as Alitalia, some budget airlines may be a better option than the long train. RyanAir flies from Rome Ciampino (CIA) to Trapani Birgi (TPS). Blue Panorama and EasyJet fly from FCO to PMO. AirOne flies from Genoa (GOA) to CTA. Blue Panorama and Meridiana fly from FCO to CTA.
Air Italy, as Tim mentioned, is actually a codeshare. The flight is operated by Meridiana which purchased AirItaly in a merger last October. The above low cost usually don't appear on search engines such as Kayak.com, therefore you should search them in their individual websites. There are also several low cost airlines search engine websites where they might appear. For example flylowcostairlines.org or europebyair.com or skyscanner.net and many others.

wayne, I travelled from FCO to PMO in September and used EasyJet (as usual). The flight was a very "easy" 1H:10M. They currently have fares listed for January as low as €25.49 (plus a few "fees" of course). They currently have three flights a day operating on that route. If you decide to book with EasyJet, be sure to read their baggage rules carefully. If your checked luggage will be over the limit, it's cheaper to pay the overweight charges at the time of booking, as it's more expensive at the gate. As with many airlines in Europe, only ONE carry-on item is allowed. That doesn't mean "one plus a personal item such as a Purse or Laptop case", it means one only of the approved size. They DO check! Were you planning to use the Airport Shuttle into Palermo? If that's the case, turn right when you exit the baggage retrieval area and look for a small booth. The fare is €6.10 (or at least it was in September). I disembarked at the Teatro Politeama stop, as that was the closest one to the Hotel. EasyJet also has flights from Nice to Rome, so that's another option. Happy travels!

Thanks eveyone. Easy Jet looks good from fco to pmo.
With a 2:15 hour gap at fco between the AF flight from MRS all should go well unless there is a strike.