When you pay higher prices for the examples you have shown there is a service enhancement involved. This certainly justifies an additional charge. In the case of paying extra for an oversized vehicle there is no such enhancement. I just completed my roundtrip on the Auto Train and witnessed the loading and unloading of vehicles. As Alan pointed out previously, SUV's and regular autos are loaded in the same carrier car. I saw no additional services performed with the loading/unloading of my SUV compared to a regular size auto. The additional fee associated to the SUV is an antiquated one and should be eliminated in my opinion.
Let me play Devil's Advocate here. The alternative to taking the auto train is driving the distance. Larger vehicles are less efficient. Therefore, it costs more to drive an SUV from Lorton to Flordia than a regular car. It would make sense that the SUV owner would be willing to pay more, because the cost of their alternative is greater. Regardless of the historical reasons for the price difference, I think it makes sense from a business perspective.
Actually, at least for me, there is another alternative. In lieu of paying the additional fee for bringing my oversized vehicle, I can bring my standard size auto and attach my luggage carrier to it. I will still be able to bring the same amount of luggage and gear as an end result.
Maybe it is me but I can't in good conscience pay a considerable higher fee for a service that does not provide any additional input by the provider.