The CodeIgniter User Guide gives this example:

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

But this has a tendency to fail for most people, who must then resort to the forums.

A more elaborate solution can be found in the CodeIgniter Forums.

<IfModule mod_rewrite.c>
   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]
</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.
      # Submitted by: ElliotHaughin
   ErrorDocument 404 /index.php
</IfModule>
   AddHandler php5-script .php


This should take care of your problem. If not shoot me a comment and I’ll see what I can do to help.