Custom Post Types Permalinks not working correctly

Hi.

For some reason the custom post types peramalinks is not working correctly.

They are showing up like this:
http://localhost/site-name/?course=maths

when I want it like this:
http://localhost/site-name/course/eyebrow-shaping-ebs

I have used the following code in my THEME [NOT PLUGIN] functions file:

function create_post_types() {
	$labels = array(
		'name'               => 'Courses',
		'singular_name'      => 'Course',
                ....more labels that are not relevent
	);

	$args = array(
		'labels'             => $labels,
		'public'             => true,
		'publicly_queryable' => true,
		'show_ui'            => true,
		'show_in_menu'       => true,
		'menu_icon'          => 'dashicons-book-alt',
		'query_var'          => true,
		'rewrite'            => array( 'slug' => 'course' ),
		'capability_type'    => 'post',
		'has_archive'        => true,
		'hierarchical'       => false,
		'menu_position'      => 5,
		'supports'           => array( 'title' )
	);

	register_post_type( 'course', $args );
}
add_action( 'init', 'create_post_types' );

I also used rewrite flush (although I think this is only needed when using custom posts within a plugin, not a theme- correct me if I’m wrong).

function rewrite_flush() {
	create_post_types();
	flush_rewrite_rules();
}
register_activation_hook( __FILE__, 'rewrite_flush' );

Please HELP!!!!