We've ridden the Auto Train several times. The comment BG posted sounds a lot like someone sent him an edited version of the same post I put on the Washington Nationals Fan Forum a couple of weeks ago because it's pretty close to verbatim what I said there. See this link. I'm glad someone found my comments there useful!
http://www.wnff.net/index.php?topic=24958.msg946499#msg946499
For us the decision to use the train has boiled down to a couple of things:
(a) If we go for a weekend it's not worth it. Takes too much time. Same goes for driving.
(b) For one week it's borderline. Two people flying and renting a car is expensive, but the time factor on either end when you drive or take the train is an issue.
(c) If we go for two weeks the train makes a lot of sense, especially since we have relatives in the Melbourne area (so if we take the train one-way coming home, we can take our time in the morning, drive the approximately one hour to Sanford, and check in for the train in early afternoon). I don't mind the long drive if we just drive the whole way, but the difference between driving and the train is that when I drive I can't do anything else other than listen to music or talk to my wife. On the train I can read a book, walk around, etc., and I can drink wine with dinner without worrying about getting back in the car and driving. Other thing is, even though in raw number of hours the train is a longer time commitment than driving, it's an overnight train. That is, if I leave home at 7 AM, I don't hit traffic, I average 70 to 75 mph, and I make three or four stops for gas/food/toilet, I'll hit Jacksonville around 6 PM (it's about 690 miles to the northern edge of that area). Orlando or Melbourne will be about another 160 to 170 miles depending on which roads you then use, so another 2.5 to 3 hours. That's a long day, or a day and a half if we stop for the night (my wife is unlikely to put up with another 3 hours in the car after 10 to 11 hours already), on which I can do nothing but drive, whereas on the train I have half a day free on each end. So an overnight train ride suddenly looks a lot better, you know?
What we've done the past few times is to take the train one way and drive the other. I can generally get 425 to 450 miles on a tank of gas (93 octane) on the highway, so I'm looking at a fillup around Florence, South Carolina, and then again when I get to my destination if I'm not going further south. Figure three tanks of gas. Let's assume gas is $4.50 a gallon and I put in 15 gallons per fillup. That would be $67.50 a fillup, $202.50 in gas one-way. I just punched up the Auto Train fare for a trip this June in coach class and it quoted me $511.00 with the AAA discount, so if I were to use the Amex points it'd be $211.00. That's pretty comparable to the cost of gas. (As I said in the other comments linked above, we tend to go for the roomette. It usually adds about $100.) To compare that to flying, last time I looked airfare to Orlando was running around $375 to $400 per person. Multiply that by two and add a rental car and you're over a thousand dollars pretty quickly. So the idea of taking the Auto Train or driving suddenly sounds a lot better as long as your trip is for a long enough time to justify it. I never sleep worth a damn on the train, even in the "roomette," but the time savings and money savings make me willing to suck up one night with minimal sleep.
One thing to bear in mind is that you should NOT plan on anything time-sensitive on the day of your arrival on the Auto Train because the trains are notoriously late on weekdays. CSX owns the tracks and so they give their own freight trains priority. There are fewer freight trains operating on weekends or around Christmastime and so at those times the train may be early. We were an hour early arriving into Lorton on the Auto Train the Thursday morning after Christmas earlier this winter. Also, as noted above, you have to wait for your car to come off. In Sanford there is a further slight delay in disembarking the train because the platform is shorter and they have to decouple some of the passenger cars and move them to the other side of the platform.
Some people try to show up at the last minute to check in their car for the trip because they think they'll be the first off. That doesn't work. The sidings in Sanford are a lot shorter than the ones in Lorton and so the car-carriers are all arranged differently.
I have never waited two hours for our car to come off, but it's possible. I have waited an hour.
BTW, the reason they insist that you have your car checked in by 3:00 PM is that they have to assemble the train. The car-carriers are all on different siding tracks with bridges between the cars and they have to close all that up, then tow the car-carriers out to the main track and couple them onto the back of the full train (and, in Sanford, they have to assemble the passenger portion of the consist as well).