Not Found
The requested URL /~username/ was not found on this server.

Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

The strange part is...that user does exist.

Also, I checked the dns zone, httpd.conf, all look good.

Code:
<VirtualHost xxx.xxx.130.xx>
ServerAlias domain.com
ServerAdmin webmaster@www.domain.com
DocumentRoot /home/username/public_html
BytesLog domlogs/domain.com-bytes_log
ServerName domain.com

User username
Group username
<IfModule mod_php4.c>
php_admin_value open_basedir "/home/username/:/usr/lib/php:/usr/local/lib/php:/tmp"
</IfModule>
<IfModule mod_php5.c>
php_admin_value open_basedir "/home/username/:/usr/lib/php:/usr/local/lib/php:/tmp"
</IfModule>
ScriptAlias /cgi-bin/ /home/username/public_html/cgi-bin/

User username
Group username
CustomLog /usr/local/apache/domlogs/domain.com combined
I ran /scripts/udpateuserdomains, restarted cpanel, named. Still shows that error.

I enabled in mod_userdir protection user ability to view via IP, still does not work.

drwxr-x--- 15 username nobody 4.0K Nov 27 21:17 public_html/

I even ran chownpublichtml.