Yes! SE starts at $139/month...pretty expensive in my opinion.
Or you are in a country that Fogcreek can't do business with
Or you want a site on a topic that FC, or their bankers, or their VC or their government don't want you to have one on
Or you want an internal secure site for your society, company, hospital, police force
This is the real win in my opinion. On the open web, the SE sites are not just about the technology -- that is quite a small part of the problem.
Internally, especially in smaller companies, involvement is less of an issue and the technology becomes are more significant part of the problem. This is where I see a lot of opportunity for Shapado.
No company is going to have it's knowledge base on someone else's servers - especially not any industry 'knowledge rich' (urghhh) enough to need an SE site