The subsidies mentioned are federal transportation (highway) spending. Without that (or even better with it redirected into mass transit) the prospect of commuting into the city by car becomes a lot less economical.
Federal mortgage subsidies are tied to single family housing as well.
I'm not sure what other "subsidies" you are talking about, but the mortgage interest deduction has nothing to do with the type of construction or zoning. Neither are FHA loan programs.
It isn't directly tied to zoning, but it provides the greatest benefit to people with expensive houses and high incomes.