If you still want your primary domain to use a root folder other than public_html, you have two options:

• Change the primary domain name on your account, then add the old primary domain as an addon domain. This way, you can pick the root folder you want for the primary domain/new addon domain. (The new primary domain will now point to public_html.)
• Use mod rewrite to automatically redirect your website visitors to a new default directory. The new folder name will appear in the URL (i.e., http://domainname.com/subfolder/).