Yeah, I'm surprised that a company whose core product could be run by three people for less than a million USD per year with room to spare for lavish company cars, somehow manages to lose $84 million USD.
Atwood and Spolsky themselves boasted repeatedly that SO, for a long time, was just a Windows server and a SQL Server with some C#.
The key element in the success of SO was not technical: it was Spolsky and Atwood leveraging already-established (Microsoft) audiences they had, to create a virtuous circle of sharing that snowballed for years.
I think OP may be referencing SO has multiple products outside the core QA site that may be more headcount-intensive or at least have more costs outside a few .NET servers and a well tuned database.
Not to mention an international presence benefiting from 24-hour on-call rotations that would benefit from international offices and other fixtures that are very expensive to maintain.
