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Well, I think technically BART and the DC Metro have more track miles, but according to https://en.wikipedia.org/wiki/List_of_United_States_rapid_tr... the "L" narrowly has the second highest ridership.

Some of that may be a difference in focus. The L barely extends outside of the city proper, and a separate rail system almost exclusively serves the suburbs.

The division of responsibilities between the rapid transit and commuter rail systems in DC and the Bay Area is different in a way that might account for both the greater total system length and the lower ridership per mile compared to Chicago's system. Or Boston's T, for that matter.

Outside of Manhattan, much of NYC's system is aboveground, too. I'm not sure it normally makes much sense to put the trains underground in any but the most densely populated areas.

I don't want to get into an argument on the definition of "subway", but Chicago's is not like what this article describes, or what is in Manhattan.

Chicago has 11.4 miles of underground subway tunnels in use. That's larger than what is described as Cincinnati's abandoned subway in the article.