Traveling from Milan to Amalfi with a return to Santa Magarita and Lake Como....

There are 14 villages and hamlets called Santa Margherita-something in Italy, but no one called Santa Margarita. I guess they have one in Mexico like we have villages named Barolo and Montalcino...
Are you visiting Santa Margherita Ligure? Not far from the Cinque Terre? The station is called "Santa Margherita Ligure-Portofino" on trenitalia.com/tcom-en

Amalfi has no train station, but in season there are Travelmar ferries going from Amalfi to Salerno where you can get on local and high speed trains.

I don't get where you would go by taxi, but I see no reason to drive in the Alps when there are trains and ferries that can do it for you.

We are heading to Santa Margherita Ligure near Portofino. Would you suggest a train or flight to Genoa from the AC ?
Thanks!

If there are flights available, take one.
Amalfi- get the train in Naples or Salerno.

We are heading to Santa Margherita Ligure near Portofino. Would you suggest a train or flight to Genoa from the AC ?

What does "AC" stand for? As you have seen, if you don't use the full place name it can be ambiguous.
With very few exceptions, a train will be quicker and more comfortable than flying within Italy. If you fly, you almost always still need a train to get to your final location.

It depends on the availability of direct flights from Naples to Genoa and on the time needed for security at the airport.
A train from Napoli Centrale to SML via Florence and Pisa takes around 7 hours... plus the time needed to get to Naples from Amalfi.

Unless you can find a direct flight from Naples to Genoa (there's typically a change in Rome), taking the train will probably be just as fast and have fewer changes. Train from Salerno is 7-8 hours with 2-3 changes, while flying involves train to Naples, bus or taxi to airport with buffer for check-in and boarding, flights from Naples to Rome and Rome to Genoa, bus or taxi to Genoa train station and train to SML. The 3 hour flying time starts to balloon quickly and requires 4-5 changes.

AC is the Amalfi Coast. That seemed to be the abbreviation others were using but absolutely right; can be misleading!

There is a non stop flight from Naples to Genoa; its 1.25 hrs. I know that we'll probably need to plan to be at the airport at least 1.5 hrs in advance. Once we land, we'll need to train to Santa Margherita Ligure so time rolled up all counts. I wonder if the train will be a scenic ride?

AC is the Amalfi Coast. That seemed to be the abbreviation others were using but absolutely right; can be misleading!

Don't worry, it's less misleading than CT for Cinque Terre. Everytime someone uses that abbreviation I think they are going to CaTania, in Sicily!

In Liguria most railways run in tunnels.

According to skyscanner.com, Volotea has 1-3 non-stops per day,( varies by day of the week) NAP-GOA