I don't think the "right of way" for tunnels is as simple and easy as the author claims. Many land rights include the soil beneath the land. While tunnels could be built below existing Federal and State owned land, many of the problems outlined for railroads by the author would happen again with acquiring the land required for tunnels.
Many of the other points in the article seem glossed over and error prone as well (e.g., simplifying the comparison between trains and trucks efficiencies to a rolling resistance coefficient and ignoring the discrepancies in weight of the vehicle an all other efficiency factors).
You're right that property rights underground can be complicated in the US, but generally speaking the easement rights needed for underground are likely to be much easier and cheaper to acquire. Someone comes and wants to give you $5000 to tunnel under your land and you don't have to move or be disrupted in any way is a much tastier proposition than losing the family farm. That's not even counting tunneling under existing road and rail rights of way which would be even easier.
It'll take a lot more than $5000 to get my permission to tunnel under my house. I'm not sure what the number would be but $5k isn't even in the ballpark. I would be concerned about things such as vibration, structural integrity, ventilation, and potential noise through the ventilation. Probably more things if gave it much thought. Depends on how deep the tunnel is, also.
Looks 5k is just a number I pulled out of my ass. The Boring tunnels are generally deep enough that these things aren’t a concern but if it’s $x plus named protection on an insurance policy, that’s still a lot cheaper than surface rights of way.
Many of the other points in the article seem glossed over and error prone as well (e.g., simplifying the comparison between trains and trucks efficiencies to a rolling resistance coefficient and ignoring the discrepancies in weight of the vehicle an all other efficiency factors).