While it's true that Super User hosts questions about operating systems, operating systems aren't the only kinds of software handled. The help center says:
If you have a question about …
- computer hardware,
- computer software, or
- personal and home computer networking
and it is not about …
- [various unsuitable things]
… then you’re in the right place to ask your question!
We have all kinds of questions on all kinds of software, from adobe-photoshop to google-chrome to thunderbird, and so on. There can be "super users" of any technology. Someone might be knowledgeable about the internals of the Windows PnP system, while another might know the advanced parts of Firefox like the back of their hand. Any kind of software used by consumers (except web apps or mobile apps) is fair game.
That's how things currently are, but why is it good/acceptable/reasonable for them to be like that? The Stack Exchange blog has a post about sizing of SE sites: Merging Season. If the communities are too small, they won't attract enough people for the site to seem buzzing with activity. Super User is very active - something pops to the top of the front page every minute or two. On the other hand, if the communities are too large, they degenerate into vats of sludge (cf. Yahoo Answers) or fizzle out because there's nobody to care about most of the subjects. Again, Super User seems to be doing great. All subjects that I see meander down the front page are well maintained.
Another reason we don't split is simply inertia. There is a vast quantity of Office questions with a happy home here; even if we wanted to, cleanly separating those out would take a ton of effort. microsoft-excel is the site's seventh most used tag!