// Flush permalinks every hour 
add_action('my_hourly_event', 'do_this_hourly');

function my_activation() {
	if ( !wp_next_scheduled( 'my_hourly_event' ) ) {
		wp_schedule_event(time(), 'hourly', 'my_hourly_event');
	}
}

add_action('wp', 'my_activation');

function do_this_hourly() {
	global $wp_rewrite;
	$wp_rewrite->flush_rules();
}