If you want to go some distance you're always paying something to do it - you can't therefore assume all means of going a distance cost the same and that factor can be ignored, though. A plane, train, bus, car, and taxi are all going to have different cost efficiencies (some more different than others) of going on a given type of trip. From a different perspective, they all require purchase, maintenance, licensing, and registration as well - but those are still part of TCO because it's part of the total cost. If you remove them for being the same type of cost rather than the same actual cost then you wouldn't really end up with much going into TCO even though the total cost of each is wildly different.

In general, you're almost certainly no longer on the path to calculating anything that should be called TCO once you've started removing costs associated with using the item. Apart from that, you're probably not on your way to a very meaningful cost comparison either.