Flight into Milan MXP, need to get to Linate

Another option is a train.
Malpensa Express (much discussed on this forum) to "Milano Centrale" station, then a High Speed train to Rome.
Train takes about 4¼ hours, two High Speed trains per hour. So, if you are lucky and get out of the airport at 13:00 (1 pm):

Depart 13:13 Malpensa Aeroporto Arrival 17:40 Roma Termini
Depart 13:43 Malpensa Aeroporto Arrival 17:55 Roma Termini
Depart 14:13 Malpensa Aeroporto Arrival 18:28 Roma Tiburtina
Depart 14:43 Malpensa Aeroporto Arrival 18:55 Roma Termini

That's right in the centre of Rome, no airport transfers.
Problem 1 is that immigration could (worst case) take 1 hour; and / or flight could be 1+ hours late. So it is best not to buy a ticket in advance, but to pay the "walk up" fare, which is €89 Milan to Rome (plus whatever it costs from the airport to Milano Centrale).
For train times and prices go to: http://www.trenitalia.com/ and select English from the menu at the top, enter "Malpensa Aeroporto" to "Roma ( Tutte Le Stazioni )", date and time.

Take a train to Rome, much easier than transferring between airports. Probably also a little faster.

It makes no sense to fly to Rome from Linate. Take the train. When you consider total time of flying, travel to and from airport -both ends, checkin and security hassle at Linate, etc. The train is better and probably cheaper. It would only make sense to fly IF your connecting flight was at MXP.

I agree with the others in that the high speed trains would be a better option. They travel at up to 300 km/h and in many cases are faster than by plane, when all is considered (travel to & from airports, check-in, security, etc). Also, that will for sure be a much more pleasant trip than by budget airline. Which airline were you planning to use from Linate?

You'll be arriving at MXP Terminal 1. From there take the Malpensa Express to Milano Centrale to connect with the high speed trains (travel time ~52 minutes). You can buy your M.E. ticket at the airport rail station. I believe there are also Kiosks there where you can buy your ticket for the Milan - Rome train.

Two important points to note.....

1. The Malpensa Express has two lines from the airport, one going to Milano Centrale and one to Milano Cadorna. BE SURE to board the correct train!
2. You MUST validate (time & date stamp) your ticket prior to boarding the train, or you'll risk hefty fines which will be collected on the spot! Note that tickets for Metro, Buses, etc. in Rome and elsewhere must also be validated.

The high speed train has compulsory seat reservations, so you must sit in the Car (Carrozza) and seats (Posti) listed on your ticket. The reservations are specific to train, date and departure time so can only be used on the ONE train listed on the ticket. If you board the wrong train by mistake, you guessed it, fines on the spot! Note that your destination station will be Roma Termini. Travel time is generally between 2H:55M and 3H:20M.

If you arrive at MXP at Noon it makes no sense to go to Linate to catch a flight at 5pm to Rome. Take the train from MXP (change at Milano Centrale) and you'll be downtown Rome long before that airplane has landed at the Rome airport.

Thanks so much, everyone! This has been really helpful. We will most likely take all of your advice and plan on taking the train.