Most people will use the train just to get the gems, no matter how much coin they may get from an order or not. I've discarded trains when I know the orders are outrageous and not worth the 5 gems as it would be too hard to get the items (iron, jewelry) and even if I could get it to the 2 gem mark, if the cost difference is too great, bye-bye train.
However, I do many of the trains that require a lot of crops, like my current one. I think there are at least 6 crops (tree crops included) and those items I could easily replace if necessary from the paper - worth the 2 to 5 gems free IMO.