Magento has an annoying problem of have both index.php and root displaying the same home page content. To redirect index.php to the root is easy.

For instance, if you want to redirect a url like http://www.example.com/index.php/ to http://www.example.com/, here is what you can do. in your page template (for example, 2columns-left.phtml) add in the following line at the very top of the file:

<?php
if ( $_SERVER['REQUEST_URI'] == "/index.php/" || $_SERVER['REQUEST_URI'] == "/index.php" ) {
    header( 'Location: http://www.example.com/' ) ;
}
?>