I previously wrote about 301 redirecting www to non www url and vice versa to avoid a possibility of getting a duplicate content penalty, but the is another scenario where you can have two identical homepages.
Google See’s your domain. say www.bettermychance.org and www.bettermychance.org/index.php as two different pages with the same content on both. so a great way to solve this problem is by putting some code in your .htaccess file
Here is what you do:
Options +FollowSymLinks
RewriteEngine on
RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php\ HTTP/
RewriteRule ^index\.php$ http://www.bettermychance.org/ [R=301,L]
Replacing my domain above for yours.
Now when anyone goes to your domain.com/index.php they will be redirected to your main URL thus eliminating the chance of a duplicate content penalty.