The problem arises in classes/class-cartflows-meta-fields.php on line 119.
$supported_product_types = array( 'simple', 'variable', 'variation', 'subscription', 'variable-subscription', 'subscription_variation' );
If you change it to the following it will work.
$supported_product_types = array( 'simple', 'variable', 'variation', 'subscription', 'variable-subscription', 'subscription_variation', 'course' );
CartFlows is restricting the product types here and is not including the ‘course’ product type. There should be some kind of filter here that integrations can hook into to let cartflow works with other woocommerce product types.