Removing index.php in url problem

[eluser]Unknown[/eluser]
I would like to remove "index.php" from url. I am using .htaccess to add this :

RewriteEngine on
RewriteBase /site
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ index.php/$1 [L]

it works and the no "index.php" url is work. However, when I am using url helper to make a hyper link. The "index.php" appears again in the link. How can I make it disappear?

* the index_page is empty.
$config['index_page'] = '';