They are not subcommunities. They are partially intersecting communities. Many of the questions on [Database administrators](http://dba.stackexchange.com/) are firmly on the database side, involving no administration at the system level. Most questions on [Webmasters](http://webmasters.stackexchange.com/) involve the page contents, not the administration of the servers. Many of the questions on [IT Security](http://security.stackexchange.com/) are not about system administration but about application security, data security, etc. The list goes on and on.

This is natural: subjects intersect, audiences intersect. You can't have a straight separation between subjects. This happens in fields that aren't computer-related as well; for example there's a [science fiction site](http://scifi.stackexchange.com/) which discusses SF [books](http://literature.stackexchange.com/) and [movies](http://movies.stackexchange.com/) (and, occasionally, SF in other media).

Across the Stack Exchange network, I'm only aware of a single case of a site whose subject is a subset of another site's: [Ask Ubuntu](http://askubuntu.com/), where all the questions would be on-topic on [Unix & Linux](http://unix.stackexchange.com/). You'll note that AU has a lot more traffic than U&L. A significant proportion of AU users don't care that there are other Linux distributions (let alone unix variants); they want an answer for their computer. They wouldn't be as satisfied with U&L answers, which often tend to be more generic at the expense of being more complex.

Grouping sites doesn't work in all cases. AU vs U&L is an example: AU superficially looks like a tag on U&L, but the target audiences are different. Beyond content, there's also the issue of moderation policies: they are not the same on every site. For example, circumventing someone else's policy is a big no-no on SF, only raises a few eyebrows on SU, and is not a concern on U&L. Different sites have different stances on “soft” questions such as literature requests or social concerns. Again, tags don't allow such differenciation.

On practical matters:

 * If you wonder where to ask your question, think which community is really focused about that subject. If it's primarily a system administration question that happens to be about a security feature on Linux, ask on SF. If it's a question on security that happens to be about a Linux feature, ask on Sec.SE. If it's a Linux question that happens to concern a security feature, ask on U&L.
 * If you have cross-site interests, which is inevitable for many people (for example, you can guess from my profile that my interests include various computer-related topics as well as science fiction and French — they aren't all going to be on one site), create a [tag filter on `stackexchange.com`](http://stackexchange.com/filters/my-filters).
 * Reputation denotes expertise in a particular topic (insert caveats here). That's why it's per-site.