This is Apche's mod_userdir feature. You can control this feature at "
Main >> Security Center >> Apache mod_userdir Tweak" in your WHM.
Add an exception to
"DefaultHost (nobody)" from the above option, to have ~user access using server hostname / IP ( that is
http://serverhostname/~user ) .
Please note that, this will limit ~access using hostname; access using any other URI will be disabled.
