It's a very rare case of a site being a subset of another. In this case, part of the justification is that there is a wide community of people who self-identify much more as Ubuntu users than as Linux users. Furthermore, even if the questions asked on AU can be asked on U&L, they would tend to gather different answers: on AU, an answer that's specific to Ubuntu running its default interface, with screenshots; on U&L, a fairly generic answer covering many distributions and tending to use the command line by default. So it's a case of having partly separate communities, and partly separate content.
Historically, the Ubuntu site was born a few weeks before the Unix site. Both were successful early on in terms of content quality and traffic. After the sites were up and running, Stack Exchange ran a poll; a majority of Ubuntu users voted against merging and a majority of Unix users voted for merging. The merge didn't happen. You can retrace the history through some blog posts:
The separate sites were kept, leaving a sour taste in some mouths and the aftermath was a push for larger Area 51 proposals: Merging Season. It didn't take.
For the record, I'm mainly a U&L user, and I voted against merging. Subsequent traffic statistics show that if there had been a single site, something would have to give: either AU's 100 questions/day would dominate U&L's 25, or most of AU's traffic wouldn't happen.