This is a really good comment thread and got me thinking.
However here in the UK I'm not sure your point about virtual subsidy quite computes. Most of the free to use parking in valuable areas is street parking outside homes. Seeing as housing costs are just a big sponge that absorbs any surplus productivity, I suspect if people had to rent or buy those parking spaces to use them then you would see a corresponding drop in house prices/rents.
It's still a subsidy because they are charging less than the market value of the most valuable possible use.