This is a great plugin, so thanks for that, but it has an annoying feature that if not monitored closely can cause a site's number of 404s to rise dramatically. The default behavior of this plugin is to include all registered custom post types and taxonomies in the XML sitemaps unless you specifically exclude them. I would argue that it makes more sense to only include the default WordPress post types and taxonomies, and instead only include custom post types if they're explicitly included.
Another alternative might be to have a flag set by the site administrator in the plugin's preferences allowing for the admin to choose whether or not to automatically include all registered custom post types and taxonomies in their sitemaps.
As WordPress gains in popularity as a CMS then there will be a lot more people using the custom post types as a way of managing content that's never meant to be directly accessible.
At the very least there should be a prominent notification accompanying the plugin letting people know about this behavior.