Longer distances should be more profitable than short, since revenue increases linearly with distance, while the overhead associated with stations stays constant. You may also be able to build straighter routes. Your bank account will go negative, but since you own infrastructure of equal worth, you will not go bankrupt.
There are other problems, though, at least with the traditional way industries order supplies. With greater distances, the latency also increases. It takes longer time from when a factory orders more supplies to the time the supplies arrives, which means that it may run out and production stops for a while. This causes vehicles carrying products away on the other side to stand still, while fixed costs still apply.
Industries have a maximum distance setting, but this doesn't always apply unfortunately.