Cycling is cleaner than any of them. So what?
...sure. But also, once you build a 5+ million person metro area you're pretty committed to it...
NYC, LA, Chicago, Dallas, Houston, Washington DC, Miami, Philadelphia, and Atlanta.
You could profitably run high-speed rail between NYC and DC, hitting Philadelphia on the way. Amtrak does run a sort of high speed service on this route.
There's a study underway for a privately funded high-speed rail connecting Dallas and Houston.
Miami to Atlanta is at the edge of what might make sense.
Sizable metro areas can decline, Detroit is now 1/3 the size that it was at its peak in the 1960s. The railway station was abandoned.
Electrified rail is a viable alternative to suburb <-> urban center commutes. Similar/better travel times are possible.
And in both cases rail is much more pleasant. E.g., ICE trains are way nicer airplanes -- anyone who thinks otherwise has never been on an ICE train or really enjoys being punished.
I also prefer DB trains to being a passenger in a car on an interstate. Trains, when well-done, are much quieter, a much smoother ride, have much more comfortable seats, and offer the option to stand up and stretch if you feel like it.
Cycling is never a replacement for either of those two use cases.
It's a viable alternative to short-haul flights. Boston to Las Vegas, San Diego, San Francisco, or Seattle is not really competitive by rail, even if the US had any high-speed rail.
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