They basically said that NYC and SF "threw the curve," and should be excluded from the analysis. Probably, the same goes for Chicago and LA.
What I find amusing, is mean commute times. I know a number of folks that live in the Atlanta and Boston areas, and they would love a 30-minute commute. I think that NYC claims a 27-minute mean commute, but everyone that I know that commutes (and I know a lot of folks that commute; both by car, and by rail), take 90 minutes to two hours.
I think they must include [very expensive] suburbs right on the city limits, to get those means; when the affordable housing is out in the bedroom communities; usually 20-50 miles away.
Also, if the commute is supposed to end at the city limits, or some fixed point, downtown, it's leaving out a significant amount of time. It can take two hours to drive from the Queens/Nassau border, to the Hudson (on a bad day -usually, it's an hour). Subway rides take a certain time, too. These are affected by proximity to stations, and how many stops a train makes.
I don't think it's a useful comparison for any sub-60 minute commute when it's a passive mode of transportation vs active.
When I lived in Manhattan, I had a ~35 minute commute by subway. I read a book every week or two, and it was far more productive than anything that happens in a 20 minute drive by car. My commute now is roughly 20 minutes, driving... and it's very stressful.
Beyond 1 hour, the time lost has greater impact on your life (socializing, household chores, family time, etc). Even still, I'd rather 90 minutes in a train than 60 behind the wheel.