Essentially, a portal site (really, a terrible way to refer to portals – see Todd’s excellent blog post on this: mindsharpblogs.com/.../923.aspx) is just a portal. A portal is a site collection that has been templatized by portal server to be a portal. When you create a top level web site, you’re creating a new site collection inside a managed path of a root site collection (the root being either a portal or a WSS-templatized site).
I know this is confusing, in part, because of the way they’ve named the elements here and partly because of the way they needed to architect the web sites in order for them to be scalable into the tens-of-thousands.
Does this help?