We can no longer change the document root for your main (primary) domain. This disables Fantastico being able to install applications, breaks existing database configurations, plus other issues. Document roots can only be changed on addon domains.
If you still want the root folder for your primary domain to be something 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.
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/).