the plugin works like this:
if your vhosts are set up like pointed out above: <VirtualHost *:80> every domain pointing at your server will be caught but if you don't have such a * vhost, you have to manually point/park/whatever the domain towards your wpmu install.
above you ask what about non-cpanel users?
what control panel is your hosting provider offering you? you must have one. it doesn't matter which one you still must point the domain towards your wpmu install.
how does wordpress.com do it?
well, you being on a shared host, share your IP with other users so if someone redirects his domain towards your IP, how would your host know that it should point towards your wpmu install and not the other guys wpmu install on the same shared host?
see? wordpress.com does only host wordpress.com on their servers so they can by default point unknown domains towards their only domain...
you on the other hand, must manually point the domain towards your wpmu install,
###pretty simplified, but it should convey the bigger picture###