Lorenzo Alberton has a quick tip for those dealing with Zend Framework applications and shared hosting:
The public directory contains all the files that should be directly accessible via the web server, so you must set your web server's document root to this directory. The problem is, in most shared hosting setups you can't change the document root. [...] To solve this problem without changing the above directory structure, you can remove the .htaccess file from the public directory, and place this one in the root directory instead.
His new .htaccess file makes use of the mod_rewrite Apache extension to force everything back into the bootstrap file for your application. You can find out more about setting up a Zend Framework application in their QuickStart guide.