Just now, I decided to price a ticket from Delray Beach, Florida (where the closest Amtrak station is to my house) to Deland, Florida (a distance of 220 miles). By car (and my car, I mean, my car, which gets 30mpg), it's a total of six hours (three there, three back) and will cost me $45 in gas (assuming $3.00/gallon, which is a bit high right now). This is doable in one day (leave by 9:00 am, arrive around noon, leave at 6:00 pm, arrive home by 9:00 pm).
The same trip, by Amtrak, costs $96 (twice my gas costs), and is impossible to do in one day. The train leaves at 9:22 am, arrives at 2:39 pm (over five hours, but more on this below). The train back leaves at 1:02 pm and right there you should see the problem---I have to stay overnight, incurring more cost. But anyway, it leaves at 1:02 pm and arrives at 8:31 pm, taking over seven hours.
The departure times assume everything goes smoothly. My first real train trip [1] from Delray Beach to Kissimmee (not quite as far as Deland) was incredible (don't get me wrong), but the train from Kissimmee back to Delray Beach was over two hours late, and I was informed that that is a common occurrence for Amtrak (it not owning the track it runs on), but had it been on time, I would have only had about half an hour in Kissimmee. Had the train from Delray Beach been late, and the train from Kissimmee been on time, I would have missed my connection.
[1] http://boston.conman.org/2015/08/05 [2]
[2] I never did find out how much my friend paid for his trip, but I assume it was the price of a car.
A train is something like 10 times more fuel efficient per passenger. It's a much less complicated machine, and carries something like 10 times as many passengers per vehicle.
It's not reasonable that a train is more expensive. It doesn't have to accelerate to 550 mph 6 miles up. Piloting it doesn't require years and years of training. Compare SFO to your local caltrain station and tell me which one has a bigger impact on ticket price.