I have the following directory structure of Codeigniter Folder. You can see that I have put all my assets in the assets folder at the root of the application.>
assets
As an addition to the answer of grim. If you have your rewrite engine on you should have the following in your root .htaccess
RewriteEngine on RewriteCond $1 !^(index\.php|assets|robots\.txt) RewriteRule ^(.*)$ index.php/$1 [PT,L]