As the title states, why does Stack Exchange (SE) have Stack Overflow (SO) its' own domain, and yet everything else is just sub-domains under SE?
Is it because SO came first, and then SE was a product of that?
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Stack Overflow isn't the only site with its own domain.
All the members of the trilogy have their own domains:
The trilogy were the first three Stack Exchange sites. You can find more information on the blog:
Custom domains was something tried for the later sites. It was given up and any custom domains created were redirected to the subdomain (e.g. askdifferent.com). You can find the full explanation for the reversal on the blog:
There are still other sites which use custom domains: