Working in an environment where hosted solutions simply aren't an option, I am grateful GH:E is around.
The actual cost per year ends up being fairly negligible when we factor in the nearly 100% removal of administration overhead that our previous VC options required.
That may have been the case initially, but I get the impression they take it very seriously now - they've hired a number of people to work on it full time, and I think it makes up a decent chunk of their overall revenue.
But there was just too much demand for GitHub Enterprise, so they made it and are charging an arm and a leg because they can.