Generally, the index page hacked with iframe code through insecure FTP/cPanel password or the system gets infected with the virus or worm from which you are managing the site. However, in case it is found the such hacking happened server wide, your hosting provider has to fix security breaches on the server. They can use custom mod_security rules to prevent such type of hacking attempt.
You can also refer the cPanel forum post regarding this issue:
http://forums.cpanel.net/showthread.php?t=62821Thanks,
Mike