I have a site with numerous custom post types that are created using a class. I was considering whether it was worth creating a custom taxonomy for each custom post type to offer a way of organizing and categorizing within that custom post type -e.g terms and tags that only apply to that post type and not others (so keeping the vernacular separate). Would that be a sensible use of taxonomies as I've seen some quite confusing (mis)use of taxonomies its seems in Wordpress.
I would base this on how many custom post types you have. If you have too many I would look into possibly re-organizing your CPTs and re-building them. If that is not possible and you do need a lot of taxonomies I would take it a step further and auto assign a taxonomy for each one of your custom post types but to answer your question this would be a good usage of taxonomies.