likely you have the wrong user.
When the domain is added on the manage domains page in the panel, it must be associated with a user. A noob mistake is that then the guy that bought the hosting says well I'lll make another user to ship off to nonlin, after all we get unlimited and everyone should have there own.... well it doesn't work that way. Only one user can manage a domains files.
When you log into THAT user, you will be at /home/USER/ and that user will have a system created folder named exactly the same as the domain name, we will use EXAMPLE.COM, put your index.html inside that folder.
Therefore /home/USER/EXAMPLE.COM/index.html will display at http://example.com
My clue that you have the WRONG user is that you didn't show the system created EXAMPLE.COM directory in your directory structure. It could also be that the customer just created a user, and never added the domain to manage domains.
See also: http://wiki.dreamhost.com/One_User_Per_Domain_Policy