There are a handful of plugins that take care of this for you (WooCommerce, iThemes exchange). Would one of them be suitable?
Thread Starter
Tim
(@liveoutloud)
I am currently using wp-ecommerce plugin.
It says it dynamically generates the download links to prevent hot linking, but i am still concerned about the folder structure itself. I heard something about putting the files above the web root but i dont know alot about coding and integrating that with the plugin just seems like it would be a massive hassle
I would only move the files if wp-ecommerce supports it… I would hope that it already has checks in place to protect your assets.
You should make sure the directory listing on your server is turned off, consider placing a blank index.php file in that folder too.
Anything beyond that and I think you will need to contact the plugin author directly: http://wordpress.org/support/plugin/wp-e-commerce