A subsidy is only a subsidy if users don't necessarily pay the full cost, and the rest is borne by some other group of people who _don't_ use the service.
Example, road network isn't paid by car owners. But non-drivers clearly benefit from the road network, is the road network subsidized?
Other example, people who rarely take the train still benefit from rail infrastructure (freight, reduced congestion etc). Is the rail network subsidized?
Do you think that it covers the cost of excess death caused by particle emissions and road fatalities?
We don't have the option to completely replace car infrastructure, but we shouldn't act like it isn't heavily subsidized.
That said, the positive externalities are also significant, but so are the positive externalities from rail traffic.
There is basically no way to compare rail vs roads and making some arguments based on that.
Of course it's possible to compare the advantages and drawbacks of different modes of transport. No society can function without roads, but it's still a question of priorities.
Most weeks I spend more hours cycling on these roads than driving.
Similar argument can be made about highways to which not everybody has (direct) access, they are not a matter of life and death for most businesses and are heavily subsidized.