Just use the alternate method for .htaccess:
Code:
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /index.php [QSA,L]
That will redirect all requests for items that don't actually exist (files and directories) to index.php.
Just be aware that you can't name a controller in ZF app that is the same name as a directory in your webspace, as mod_rewrite will never direct it at your ZF app.
Hope that answers your question.