I like the train, but I wouldn't do this one again. We bought a package with the train, bus to ferry and ferry included. The train was fine, really kinda fun, but hanging around early early in the morning waiting for what turned out to be a very late bus was no fun. And neither was arriving at the ferry landing at Samui, and learning, a little too late, that we should have grabbed a cab immediately, 'cause the terminal is nowhere and once the folks meeting the ferry are gone, after five minutes, you are trapped. Finally got a ride to a town, but it was rather stressful.
The flights do have a bunch of ripoff fees and charges, but, especially if booked in advance or as part of a package are a decent deal. And, you get free bananas at the airport.
Take the plane.