I'm pretty sure those sites are much more popular, and have better categorization for advertising targeting. You can charge a lot more for ads in /r/Television, /r/movies, and /r/trucks than you can on the generic MeFi homepage.

Reddit isn't profitable yet but is much larger and keeps its staff relatively small compared to its traffic volume.

For one I have never heard of MetaFilter and I can't understand what it is by browsing the site.

More users, more user engagement, more valuable content.