If you DO NOT FLY, why were you even comparing flying vs. taking the train? It's moot. You're going to take a train regardless, so why bother to compare them ...
My daughter had gone to NY with a friend a few months before this. They flew. The flights got messed up and the airline gave them some vouchers. My daughter wanted to go back to NY to do some things she did not get to do on the first trip. She did not want to go by herself so she asked me, "What would it take to get you on a plane?" I was willing to "try" if I could take some sort of sedative that would make it so I could manage to accompany her. While looking for flights with that airline she could not find any that had reasonable prices within her budget - even with the vouchers. She also could not find any affordable flights with any other carriers.
While looking for options, we took a look at Amtrak. Up to that time we had not taken a train before and were NOT "going to take a train regardless". We had not even thought of taking a train. While researching prices, and we're really not sure why, we decided to see what a train would cost. It was only after comparing the cost that we decided the train was a viable option.
It has only been after that trip that I have started riding the train.
It's difficult to compare the two when you have all of the restrictions you listed. It's an anecdote, at best.
Other than me not wanting to fly, what else on that list would preclude a plane and make the comparison "difficult"? We still live the same distance from JIA as we do from JAX. We always work from a budget ... we were not paying with credit cards. Someone needs to drop us off regardless of the mode of travel. We did not set the departure times. Even if we had flown, it would have been coach. Not having to pay for luggage and the walking distance were not "restrictions" ... just nice perks when it came to the train.
@Qalpa: When was this? The idea of a flight leaving JAX (the airport) at 0300 is very odd to my mind under normal circumstances, especially en route to Atlanta.
This was back in 2011, If I remember correctly. I'm not sure - but, I think the airline was American. We were using the Internet to price shop and book. We did the same for Amtrak. She was able to get a room/car deal through Expedia (best price for the deals) but, when she added a flight, not only were the options on airlines that she did not have the vouchers for, the total cost exceeded the combined price of the room/car deal and train tickets (round trip)
Prices and flight times may be different now. At the time, the price that came closest to the cost of taking Amtrak was the "redeye" that left around 3 AM.
Since that time, I have found that, since I like riding the train, I can travel a little more often than I used to - especially since I am fine riding coach. I used to drive if I went somewhere. At my age, that is tiring and I really don't want to put all those miles on my vehicle. If I have to rent a car, drive the miles, stay in a motel/hotel because I can't drive 24 hours straight, I might as well take the train and relax.