On the other hand you cannot re-sell every coach seat for every slot along the full length of the trip. Maybe you have close to 100% occupancy as the train leaves LAX but at intermediate stops after that more people may tend to get off than get on. So a coach seat may be empty for some time before somebody else joins the train to occupy it (if at all). End to end passengers thus make it easier to gain high occupancy rates and are thus the more lucrative market. I guess this is why Iowa Pacific is offering only end end fares.
Also, I don't know how much it actually costs Amtrak to sell and issue a ticket. So just because two short trips cost more than one long one does not mean Amtrak is making more money on it. Furthermore, intermediate stops cost money (it costs fuel to stop and re-start the train, it costs time, the station has to be looked after, cleaned, maybe staffed, regularly inspected etc). I believe many of the smaller stops do not come anywhere near to paying their way. I am not saying they should be closed, but from a purely finnacial perspective, I think end to end passengers have a higher fare to cost ration.
I don't have specific numbers, but my general experience says your assessment is wrong.
For one, Amtrak pays very little rent at many of the smaller intermediate stops. If the stop is unstaffed, then the general cost of upkeep of that stop is very close to nothing. If it's a small stop, then the time penalty for stopping there is generally very small (three to four minutes). Having seen some analysis of stopping vs. not stopping, in most cases (excluding premium/time-sensitive service such as the Acela, and stations that are too close together to the point where they cannibalize their own market) the lost revenue from not stopping exceeds any small cost saving from skipping the stop, and added revenue from the faster trip doesn't make up for it.
The cost to issue a ticket (assuming that all ticketing infrastructure is already in place) is next to nothing. With e-ticketing, it will be even lower.
Iowa Pacific is not Amtrak. They are mainly a tourist-oriented railroad, and don't have the on-and-off transportation function that an Amtrak train does.
As Johnny pointed out with a few examples, the fares for end-to-end trips tend to be lower than if you buy separate tickets, breaking at an intermediate point. Therefore, the yield is higher on shorter-distance trips than longer-distance ones. Selling a train out with end-to-end tickets may give you high occupancy, but it won't necessarily generate the highest revenue.
And while there is no guarantee that you're going to resell a specific seat, general experience shows that the seats do resell. You're not going to have 100% occupancy for 100% of the trip, but that's not a realistic expectation, anyway.
Using the Coast Starlight as an example, the train has several stops with significant turnover, including San Jose, Oakland, Sacramento and Portland.
The train hits its peak a couple of different times during the route, and the total passengers to be carried for today's 14 is 2.5 times its peak capacity.
There's no way you'd achieve the same revenue if you only sold LAX-SEA tickets on that trip.