Ten days in October

Timing could be critical here. How many nights are you spending in Italy, and on what date are you arriving?

10 nights beginning Oct 13,2017

Given your flight plans in and out of Rome, and your very short stay I would ditch Lake Como. That's too far and too much. Also consider that October is statistically a very wet month toward the end of the month, therefore may not be ideal for lake, mountain or coastal locations.
You should go to Florence straight upon landing. Spend a few nights there. Then 5 Terre, for 2 nights (weather permitting). Lastly back to Rome for your last 3 or 4 nights.
I don't know if you've been to Venice before, but in my opinion, that would be a must.

You've only got ten days (9 nights?), and because of that...if you're dead set on those 3 destinations, I think you've got to bite the bullet and upon arrival at Rome Fiumicino, take the 3+ hour flight to Milan Malpensa. It's another 2 hours, 15 minutes by train from Milano Centrale station to Bellagio on Como, so that would be as you say a grueling day of travel, but doable, and then you'd be done with it.

Next problem is how to get to Cinque Terre. Train is around 6 hours, through Genoa, brutal. You can rent a car and drive it in a little over 3 hours, but you'll really have to research about ZTL areas and frankly whether it's feasible to do that. C.T. to Rome is a 3 hour Eurostar ride, no problem there.

My point is that for a short trip like this with flying in and out of Rome, you're going to be on the road an awful lot with this itinerary. If you haven't been to Italy before, frankly I'd scrap both Como and Cinque Terre and stay between Florence to the north and Sorrento/Amalfi Coast to the south.

You could take the train upon arrival at Fiumicino to Florence, boom, you're there in 90 minutes, not much worse for wear. Work off jet lag in wonderful Florence for 3 nights, then 4 hours by train to the Amalfi Coast or Sorrento for 3 nights, finally ending up in Rome--a 2+ hour train ride--for 3 nights. A lot less time traveling around, more time to see what's at your destinations.

We're traveling to Italy early next year, staying 11 nights and decided to make this a 'chill' trip with 6 nights Rome, 5 nights Sorrento--flying into Rome, out of Naples.

With only that time I would do Rome and Florence only and take a train to Florence immediately on arrival and finish in Rome. From Florence you can visit Siena and Pisa and Lucca easily if you wish. From Rome you can do Ostia Antica, Orvieto and/or Tivoli if you like.

Thank you. Actually 11 days and 10 nights. I've been to florence three times and as much as I love it I think I need to explore other places. Makes sense to rethink ( and drop) Lake Como but I've never been to CT and would love to see it. The point of reducing travel time is well taken. Having said that not sure if Venice would work but I've never been. More thoughts are appreciated

Roberto -you'll be pleased to know that I am visiting San Francisco in May and staying there the entire week. No grueling side trips!

OK, then it's much more sane for you if you drop Como. Omitting Florence, take the Leonardo Express from Fiumicino to Roma Termini station for the less-than-3-hour ride to La Spezia on the C.T. Stay as long as you like there, maybe consider as you say Lucca for a night--along the train line, and if you haven't been, think about Orvieto on the way down to Rome.

There are frequent 4:38 rail connections to Venice.

Edited to add: That's the time from Fiumicino.

Now that I know more about you and your trip, I can better advise you.
Jay's plan to fly to Malpensa to go to lake Como is too crazy to even consider. Malpensa is far. and I think there are very few flights to MXP from FCO, maybe just Alitalia and EasyJet. Flying to Bergamo (Ryanai, but only from Ciampino) would make more sense, or better yet to Milan Linate (Alitalia). However, depending on flight connections, taking the 2:45 min train ride from Roma Termini to Milano Centrale might be just as fast since you need to go to the Milano Centrale.
Dropping Lake Como for Venice is what I would do, considering you have never been to Venice.
This is the itinerary I would do:
Upon landing, take train to Venice. There are two trains going to Venice directly from the Rome FCO airport at 11:08 and 15:08. If not suitable there are plenty (at least one per hour) departing from Roma Termini (Rome main station). The train ride is under 4 hours (excellent to sleep off the jetlag).
Venice: 3 nights
train back to Florence (2 hrs)
Florence: 1-2 nights (or more if you want to visit other Tuscan towns or if weather not good for Cinque Terre)
train Florence to Cinque Terre (2.5 hours)
Cinque Terre: 2 nights
train Cinque Terre to Rome (coastal route)(4+ hours)
Rome: at least 3 nights if your first time.
Fly back home

You could also do the exact opposite. Up to you.

Tarquinia, Orbetello, Siena, Orvieto, Perugia are other places worth a visit and not too far from Rome.
Another cool and cheap way to visit Italy, if you are 2-4 is to use blablacar, do you know it?

10 nights is 9 days not 11 -- the day of arrival and departure are worthless. If you have been to florence many times then it makes sense to try something else -- but with so little time, I would have two major stops. If you haven't been to Rome before, I would not stop there for fewer than 5 nights -- and might then choose one or maybe two other area for 2 and 3 nights each.

Thanks for the suggestions and ideas.... sound like dropping Lake Como for Venice makes logistical sense. Any ideas on alternatives to CT? Is CT becoming overvisited and over touristed.....? if so... have any suggestions for a similar but less popular coastal location ?
thank you