Associate users with Custom Post Type and list associated users

You have to create a custom taxonomy:

add_action( 'init', function(){
    register_taxonomy( 'program', 'your_post_type', array() );
});

To get users associated with a program, get all posts that have your desired program term:

$query = new WP_Query( array(
    'post_type' => 'your_post_type',
    'tax_query' => array(
        array(
            'taxonomy' => 'program',
            'field'    => 'name',
            'terms'    => 'your_program_name',
        ),
    ),
) );

Now get all the result posts authors and that would give you the users associated to that specific program.

$posts = $query->posts;

foreach($posts as $post) {
    $author = $post->post_author;
}