Seriously, I can see your point. It's like going into a grocery store to buy a half gallon of milk and I was charged one dollar whereas you were charged three dollars. That's certainly not fair to you!
It's like a sale where quantities are limited. The first X customers get the low price, the rest pay more.
It may suck sometimes, but it's a fair way of pricing fares. It's certainly better than a flat price. People who can/want to pay less than average can do so if they're flexible with travel dates/times and advance booking.
Honestly, looking at availability in the next few days, I can say that WAS-SDL is too cheap, it's not available at any price. The next open room is on the 20th, almost a week away. If anything this indicates that Amtrak really needs to increase fares (or increase capacity). In the short term a capacity increase is basically impossible.