codeignitor removes index.php

Ok, try

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /

    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d

    RewriteRule ^(.*)$ /index.php?/$1 [L] <-- do not forget the ? after index.php!
</IfModule>

<IfModule !mod_rewrite.c>
    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.

    ErrorDocument 404 /index.php</IfModule> 

in config.php set

$config['index_page'] = "";$config['uri_protocol']    = "AUTO"; 

With this htaccess index.php-hiding works for me with PHP4 and PHP5 running PHP as a CGI