I use fcgid and use the same htaccess you are (with the ?), AND use query strings (and superglobal $_GET is available and populated). The only difference I see is I have mine set like:
PHP Code:
$config['uri_protocol'] = 'REQUEST_URI';
$config['allow_get_array'] = TRUE; $config['enable_query_strings'] = TRUE; //note I'm not using ?c=controller&m=method etc, just regular /controller/method urls