Yes, setting the $object_type, the second argument in the register_taxonomy function, set the value to an array including your custom post type slug and post.
register_taxonomy($taxonomy, array('post','your-custom-post-type-slug'), $args);
Review: http://codex.wordpress.org/Function_Reference/register_taxonomy
Also check out my plugin http://wordpress.org/extend/plugins/reed-write/. It makes custom post types and custom taxonomies a breeze.