This is issue is addressed on stackoverflow.com in this article “Where / What is the Package Explorer in Eclipse PDT” here:

http://stackoverflow.com/questions/619455/
    where-what-is-the-package-explorer-in-eclipse-pdt

VonC [http://stackoverflow.com/users/6309/vonc] writes: “At the top of the PHP Explorer, there are a few toolbar buttons. Clicking the down arrow brings up a context menu. I choose the filters… menu item. By default, ‘name filter patterns’ was not checked. .* files and server projects were selected in the second box. This makes sense why I was not seeing my .htaccess file.”