How to set taxonomy in custom plugin?

You might need to resave your permalinks. Just press the Save button on the permalink settings:
/wp-admin/options-permalink.php

Otherwise, your code works after cleaning up just a couple of typos:

function post_type_questionnaire()
{
    $labels = array(
        'name' => _x('Questionnaire', 'post type general name'),
        'singular_name' => _x('Questionnaire', 'post type singular name'),
        'add_new' => _x('Add New Question', 'questionnaire'),
        'add_new_item' => __('Add New Questionnaire')
    );

     $args = array(
            'labels' => $labels,
            'public' => true,
            'publicly_queryable' => true,
            'show_ui' => true,
            'query_var' => true,
            'rewrite' => false,
            '_builtin' => false, // It's a custom post type, not built in!
            'capability_type' => 'post',
            'hierarchical' => false,
            'menu_position' => null,
            'supports' => array(
                'title',
                //'editor',
                /*'excerpt',
                'thumbnail',
                'trackbacks',
                'custom-fields',
                'comments',
                'revisions',
                'author',
                'page-attributes'*/
    ));

    register_post_type('questionnaire',$args);

}
add_action('init', 'post_type_questionnaire');



function create_questionnaire_taxanomies(){
    register_taxonomy('qcategories','questionnaire', array(
        'hierarchical'=>true,
        'label'=>'Questionnaire Categories',
        'rewrite' => array( 'slug' => 'questionnaire' )
    ));
}

add_action('init', 'create_questionnaire_taxanomies',0);

This template code had a few typos, but it would have thrown an error:

$atts["name"] = 'stackexchange';

$args = array(
    'post_type' => 'questionnaire',
    'posts_per_page' => -1,
    'tax_query' => array(
        array(
            'taxonomy' => 'qcategories',
            'field'    => 'slug',
            'terms'     => $atts["name"]
        )
    )
 );
 $query = new WP_Query($args);
 if ( $query->have_posts() ) { ?>
 <?php while ( $query->have_posts() ) : $query->the_post(); ?>

<?php the_title(); ?>

 <?php endwhile; ?>

 <?php } ?>