(I am new to Codeigniter, so I don't know if this is the best advice)
I keep publicly available files in my public folder. It is logical for them to be there, and I don't want to use Codeigniter for something I don't need to use it for.
The directory tree looks likes this:
The only files I keep in /public/ are Codeigniter's index.php, and my .htaccess file:
RewriteEngine On
RewriteBase /
RewriteRule ^css/ - [L]
RewriteRule ^img/ - [L]
RewriteRule ^js/ - [L]
RewriteRule ^index.php(.*)$ - [L]
RewriteRule ^(.*)$ /index.php?/$1 [L]