to me, as a user of public transit, they just seem somehow more pleasant, in a way I can't really make sense of. I strongly dislike riding in buses and try to avoid it, whether part of transit systems, Greyhound/Peter Pan, or even high-end charter buses.
maybe if you had electric (no exhaust, quiet) buses with frequent reliable service, dedicated lanes almost everywhere, nice bus stops without hostile architecture, I wouldn't feel such a strong preference, but I'm not sure.
I'm wondering whether it's not just that I subconsciously dislike getting jostled around and feeling slightly carsick.
Second, in many cities, trains actually predate the highways.
Third, trains have super high capacity, as do subways and light rail. You need more buses to keep up. However, buses are cheap, and there are things like extra-long articulating buses and double-deckers that can be used on high-volume or long-haul routes. I think buses actually have a practical edge here: instead of trains coming every hour, you could have a big bus come every 10 minutes, which smoothes out load at end stations. And if one breaks down, the other buses can just drive around it. If a subway breaks down in New York, it can cause delays that ripple out to the whole system.
Trains are excellent for dense urban environments and better yet when integrated with another modes. I take Berlin as an example: You have fare zones and S/U-Bahn everywhere in the city center extending for to Potsdam, etc., trams in the former east, buses on the less dense parts of the city. Also trivial access to regional and long-distance trains. And it also disproves the typical excuse "You can't do that in an old city": some U-Bahn lines exists since 1902, the city got devastated by war and then there was the DDR. The reunification needed a lot of work and yet the system survived. Took me a long time to notice there was no Ubers, maybe because it was not that advantageous for people to use it and Uber Inc. just gave up instead of fighting city regulations, as they did everywhere).
I compare with the systems from my native Brazil, where public transportation ranges from pathetic inefficient on big cities to non-existent in small towns. Hell, I really miss Berlin.