http://benjaminmock.de/codeigniter-auf-der-konsole-kommandozeile/

    RewriteEngine On
    RewriteBase /

    #Removes access to the system folder by users.
    #Additionally this will allow you to create a System.php controller,
    #previously this would not have been possible.
    #'system' can be replaced if you have renamed your system folder.
    RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]

    #Checks to see if the user is attempting to access a valid file,
    #such as an image or css document, if this isn't true it sends the
    #request to index.php
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php?/$1 [L]



    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.
    # Submitted by: ElliotHaughin

    ErrorDocument 404 /index.php

Jetzt muss man folgende Änderungen in der system/application/config/config.php vornehmen

#$config['index_page'] = "index.php";
$config['index_page'] = "";
...
#$config['rewrite_short_tags'] = FALSE;
$config['rewrite_short_tags'] = TRUE;

Das wars

$config['base_url'] = "http://".$_SERVER['HTTP_HOST'] . preg_replace('@/+$@','',dirname($_SERVER['SCRIPT_NAME'])).'/';

Quelle: http://www.includemedia.de/de/magazin/codeigniter-erste-schritte/