Even though this question seems to be quite old, will post an answer for someone who reaches in here searching.
SET @count = 0;
UPDATE `users` SET `users`.`id` = @count:= @count + 1;
If the column is used as a foreign key in other tables, make sure you use ON UPDATE CASCADE instead of the default ON UPDATE NO ACTION for the foreign key relationship in those tables.
Further, in order to reset the AUTO_INCREMENT count, you can immediately issue the following statement.
ALTER TABLE `users` AUTO_INCREMENT = 1;
For MySQLs it will reset the value to MAX(id) + 1.