https://en.wikipedia.org/wiki/Feist_Publications,_Inc.,_v._R....
https://en.wikisource.org/wiki/Feist_Publications_v._Rural_T...
In this case I think the MTA is still wrong though, just not for this reason.
The visualization rules for "transit map" are more open to interpretation than for "pie chart", but if you look at the maps for London, Paris, Shanghai, Washington DC, Chicago, etc., they are almost self-evident:
1. Represent major stations as white circles with black outlines.
2. Represent service lines with easily distinguishable colors.
3. Constrain lines to angles divisible by 45 degrees (Paris divisible by 30 degrees).
4. Represent non-standard service with a dashed, dotted, or broken line.
5. Stations that are connected by pedestrian access are connected on the map. Minor stations, without service interchanges, may be represented by a smaller white dot or a tick mark.
Apply the rules to the facts, and the map appears. Some human tweaking may be necessary for clarity, and that is the only opportunity for copyrightable creativity to creep in.
MTA would need to assert a particular map feature that cannot be derived from applying transit map rules to the MTA transit facts. They did not.
A map isn't "naked facts", maps can certainly be copyright protected.
If the artist gleaned facts from the official MTA map, and re-represented them on his own map, that does not make his a derivative work, even if the facts came solely from the map. The facts also could have come from riding every line and noting the station names and locations.
It's like copying a phone book. You can take numbers from AT&T's customer directory and put them in your own phone book, because that's all facts. There's no creative representation there. If the phone book represented the numbers in hand-drawn calligraphy, that visual representation would be protected, but not the factual content; you could still copy the names and numbers and re-render them in your own typeface.
Fair use doesn't even come into it. Naked facts are non-copyrightable. They have no protections whatsoever. Facts are public domain.