Correct, most people only count the cost of the gas in their car when they comparison shop. And one cannot do that if you want a true comparison. The IRS tells us that all that other stuff along with gas means that it costs 55.5 cents per mile to operate your car. AAA calculates 58.5 cents per mile.
And none of the above numbers includes anything for the massive amount of subsidies that are poured into our streets & highways. We drivers only cover half the costs of our roads via fuel taxes and other direct fees. That means that the other half slides out of your pocket via other taxes, like Income, Sales, and Property taxes.
There is no free ride, you're paying for it one way or the other. The problem is that again, most people fail to consider all the expenses when comparison shopping. They just look at the easy stuff.
The problem with 55 (or 58) cents per mile is that 1) that is an average, so a budget-conscious person can likely bring their expenses well below that, and 2) these numbers often seem to figure costs that are irrelevant to
driving a car, and are more factors of simply
owning a car. So you don't save 55 cents per mile by not driving your car unless you don't actually own a car. Once you stop owning a car, then obviously mass transit becomes the more affordable option because paying for mass transit for any given trip is likely cheaper than purchasing a car.
I think it's great to consider subsidies and how the way are taxes are spent affects out transportation infrastructure. But when you're comparison shopping between transportation options for specific trips, it's irrelevant. I don't get to say, "I took the train, so please return the tax money of mine that you would have spent on roads."
I have no doubt that our transportation system would look vastly different if we didn't pour a disproportionate amount of money into personal transportation-oriented projects, but we do, and that only adds to the idea that on a per-trip basis, driving will often be cheaper. Your tax money ends up in those roads regardless. You don't save it by not driving on them.
So I agree that just figuring gas is simplistic and ignores other factors, but I also think that many of the attempts to figure the "true" cost of driving are also unrealistic. I'm planning a trip this summer, and I hope to return on Amtrak, by myself. Even then, if I had a car at my disposal, it would possibly be cheaper to drive. On the way up, I am sharing a car with two other people, and on that trip it will definitely be cheaper to drive. Cheaper then flying, cheaper then a train, cheaper then a bus. It may be that this is a matter how tax money is spent to fund one form of transportation over another, but it doesn't change the fact that it seems strange to find that I can get 3 people across 600 miles for less money then mass transit can move 2. Maybe it's simple economics, maybe it's wrapped up in complexities of transportation spending, but whatever the reason, it runs contrary to how I
feel like mass transit should work.