The fastest train is 6 hours, so a flight won’t save much time. Any flight takes 4 1/2 to 5 hours with getting to/from airports (the airport bus usually leaves from the train station), check-in time, security time, flight time. Timing is as important as time. If the flight is at 1:30 PM , you’re going to have to start for the airport at 10:30 or 11:00, so you really can’t do any sight-seeing stuff before. You won’t actually get into Venice proper until around 4:00 PM — maybe even later if I’m right about the location of the airport most lowfare airlines use for “Venice.” You’ve still got plenty of daylight, but most museums, etc. will be closing. The train at 15:16 or 17:16 will allow time for sightseeing in Naples. The train at 7:16 that arrives at 13:17 whcih would allow a “canal cruise” on the vaporetto from the train station and some time at San Marco in the afternoon. There’s also an overnight train on this route.

Another issue is flexibility. You can change your plans at the last minute with the train. You’ll need to commit to your flight schedule weeks in advance.

My rule of thumb for a 6 hour train would be to take the train unless flying is significantly cheaper after you add the bus rides to and from the airports, taxes, booking fees, baggage fees, etc. into your calculation. Look for specials on the train fare at www.trenitalia.com