<?php
class Rewritetax {

    function Rewritetax() {
        add_action( 'generate_rewrite_rules', array(&$this, 'rewriteRules') );
        add_action( 'init', array(&$this, 'flushRules') );
    }

    /**
     * flush rules
     */
    function flushRules(){
        global $wp_rewrite;
        $wp_rewrite->flush_rules();
    }

    /**
     * Rewrite rule for taxonomy
     */
    function rewriteRules( $wp_rewrite ) {
        $new_rules = array(
            'http://mytaxonomy.domain.com/([^/]+)?$' => 'index.php?mytaxonomy='. $wp_rewrite->preg_index(1),

        );
        $wp_rewrite->rules = $new_rules + $wp_rewrite->rules;
    }
}
new Rewritetax();
?>