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.
In this case I think the MTA is still wrong though, just not for this reason.