All of my URLs on my Magento installation require index.php in them, like:
http://example.com/index.php/admin/ http://example.com/index.php/customer/account/
I tried everything on the post but nothing had worked. I then changed the .htaccess snippet that ErJab put up to read:
RewriteRule ^(.*)$ 'folder_name'/index.php/$1 [L]
The above line fixed it for me. where *folder_name* is the magento root folder.
Hope this helps!