If you have a folder which you need to access in the standard way without your Zend Controller handling it for you (maybe a direct file download outside of your Zend web application), the easiest and quickest way to do this is to simply create a .htaccess file inside the folder you want your Zend controller to ignore and populate it with:
RewriteEngine Off
Because .htaccess files work in a cascading manner, this will overwrite the Zend controller .htaccess file in the root folder, in essence turning off mod_rewrite and thus giving you full control over the folder in terms of Apache now serving it as how it normally would.
Quick and easy.
(There are of course loads of other ways to do this, like implementing something like “RewriteRule ^(admin|user)($|/) – [L]” – if you want to ignore folders admin or user – at the top of your main Zend .htaccess file in root, but I like the above as a particularly quick and easy way to simply ignore a specific directory!)