As far as I know, the main public policy benefit of the pre-tax parking subsidy is that it frees employers in lower-cost areas from the burden of calculating a fair-market dollar value on space provided in the company parking lot and withholding an appropriate amount of tax on that value from employee paychecks. In higher-cost areas, parking is treated as a taxable benefit only to the extent that it exceeds $250/month in value.
For a variety of reasons I would argue that the $250 limit is a higher than prudent and should in no cases be higher than the public transit subsidy limit. Still, some level of tax-free parking allowance makes a lot of sense in order to reduce administrative reporting burdens on fringe benefits of minimal value.