Subsites are an important concept for site management. Expression Web treats subsites as though they were completely independent sites regardless of the folder or site that contains them.
One reason that you might want to segregate certain folders in a site as subsites: you might have a large number of files within those folders that don’t change as often as the other files in the root of the site. There’s no reason to wait for a long file-comparison cycle during an Expression Web publishing session when you know that the files haven’t changed. Also, you might want to publish a segment of your site via the Secure Sockets Layer (SSL/HTTPS) if it contains sensitive files such as e-commerce site configuration or database files.