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Just because you prioritize transit in cities, doesn't mean that transport costs in general rise. Transportation between cities can remain car driven as those are inherently sparse areas anyway; you don't need to reduce use of all types of cars in cities, industrial use / deliveries can still exist in those systems anyway; and as a long term idea, self driving deliveries may also drive some of these costs later on. Additionally, while cost of transport rises for car commuters, it very well may fall for transit ones and especially for those car commuters who switch to transit. So it's not a given that prices would uniformly rise.

The cost of driving would rise, but the viability of other modes would also increase, and those other modes are generally much cheaper than driving. Note how Americans spend close to double the share of their income on transportation as the Japanese do: https://www.bls.gov/opub/btn/archive/how-do-us-expenditures-...

If food needs to be more subsidized, then it should be subsidized more directly, rather than with broad transportation subsidies that create perverse incentives for unrelated activities.