Protecting Custom Taxonomies in Protected Content

Is there a way to protect taxonomy categories registered in my WP Theme? For instance, w/ The Protected Content Plugin, I was able to protect post categories, but it seems I can only protect custom post types at the general level and not by the taxonomies I have those CPTs categorized by. I expected since you can protect post categories, protecting CPT taxonomies would be possible, but they do not appear under the option for categories to protect.