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I am not sure how it was calculated but the article did do that (but it seems like an underestimation):

"True, there’s also a tax benefit for mass-transit commuters that costs the government about $1.3 billion a year. TransitCenter says that while it’s good as far as it goes, “it is overshadowed by the parking tax benefit’s much larger adverse impact.”"

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You're correct but this tidbit also exposes the article's limited scope. It's sweeping the cost of public transportation under the rug and then providing unsubstantiated opinion on the "adverse impact" of the thing the author doesn't like.

To be clear I'm not arguing for or against parking or public transportation. But I do think we should be forming policies with more data and less opinion.

That's not quite the same thing. What you quoted is referring to the IRS tax exemption for the first $255 per month spent on approved commuting costs (parking and mass transit).

What mgreg refers to is the direct money that is used to fund/subsidize the cost of operating bus/train networks in urban areas. The cost of those tickets are less than they would be without the subsidies.

These are two totally separate things.

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