The only reason that taxis have been able to achieve any decent utilization at all is the medallion system which greatly restricts supply. Without artificially constraining supply at the expense of consumer demand, taxi utilization would be abysmal.
Admittedly, it is probably better to charge all vehicles for entering the most congested areas by their size (i.e. trucks pay more) than it is to pick and choose by artificially limiting just some types of vehicles while allowing unlimited numbers of others.