The trouble comes when you segment content to subdomain.site.com. The domain authority engines assign to a root domain may not always pass to all the subdomains, so you end up with subpar rankings to what you could earn.
As an example, we launched the Beginner's Guide to SEO on guides.seomoz.org and moved it after a few months to www.seomoz.org/beginners-guide-to-seo (where it currently lives). It had earned tons of links prior to that move, but the day after the 301 back to the main domain (away from the guides subdomain), it jumped to #1 rankings for all sorts of terms, including "seo guide" (recently got beat out by Google's SEO guide and is now #2). This was a good illustration of the power of keeping content in a single sub/root domain location for us.