I’m looking for a way to make the plugin autodiscover custom post types (CPTs) used by your site and make sure that the PMPro meta box shows up on each page. In the mean time, You can add code like this to your active theme’s functions.php (or in a stand alone plugin) to get the meta box showing up for your CPTs:
Update: I am no longer “looking for a way to make the plugin autodiscover CPTs”. It doesn’t really make sense because we have no way of knowing what the CPT is or how to protect it for members. They are by definition custom. Adding the checkboxes to a CPT would only be the first step to locking down a CPT. For example, if an ecommerce product were marked for members only, does this mean users shouldn’t see the product at all? Or should they just not be allowed to purchase it or add it to their cart? Should the product show up in searches? etc etc
Still the code above is useful for plugin developers who want to add the checkboxes to their CPTs and are ready to take the next steps to lock down their CPTs. By default, PMPro will still filter anything output through the the_content() function. You will want to either use code like this to redirect away from member content or update your theme/etc to lock down the CPT content appropriately.
Our strategy now is to work with plugin developers to help them update their plugins to support Paid Memberships Pro or develop official addons for popular plugins with CPTs (bbPress, BuddyPress, ecommerce plugins).