That is part of the problem. You are only comparing the costs that the consumer pays -- when the overall costs are compared, I'd bet that air travel is actually grossly inefficient. Remember, when you look at the total performance of the entire airline industry since it began, the industry is still operating in the red! After 75 years or so!
I'm sure you are right. There are a ton of hidden costs in air and interstate use that are hard to count. Imagine how expensive a bus ride would be if the bus company had to own the whole road from point to point b or lease any part that it didn't own. Air doesn't have to worry about that cost but it has a lot of other costs. If we federalize safety, we will all be paying that. Imagine the cost of a bus ride if you had to have a bus marshal and 3 levels of baggage check in and an FAA and all that stuff too. It would be nifty if the gmt had to match money spent on interstate systems with rail systems that were free for all railroads to use. Then you would see the competition equalized.