I work for a company that makes Orphan drugs. Yes, they're ridiculously expensive. The reason is that the number of patients for our drugs number in the couple of thousands globally. Our workforce to run the entire plant, do QA, maintenance, regulatory administration and production processes etc numbers in the several hundreds. Those people need to be paid every month by what a couple thousand people pay for their meds every month.
And that is without taking into account that this entire plant was built for making this drug, which was an investment of hundreds of millions of dollars, with several millions annually for upkeep and maintenance.
I agree that we probably make a decent profit or we wouldn't be doing it.
However, if subsidizing we to stop, we'd just stop making it because with the numbers I mentioned above, it is impossible to make our drugs in a manner that would be affordable without it. And that would mean those people would simply die.