I believe it's a population density issue. NYC's is 27,083 people per square mile, SF is 15,834 and KC is 1,406. NYC and SF are also heavily traveled (tourism, visitors, etc.) so you're serving that many more people on top of the resident population, and are open to that much more resource demand & potential abuse (don't forget), which overwhelms a lot of small businesses. Also, because these cities have such high rents and cost-of-living, those businesses require rapid turnover to make the sales needed to survive, and offering someone wi-fi access for free means they just hang around, slowing customer turnover and blocking new ones. (Hell, New York has had blackouts that have forced businesses to close for good -- it's not pretty.)

Paying for wi-fi doesn't just fund infrastructure and balance out the sag in turnover, it also weeds out the leechers (both in the store and in the 4 office buildings surrounding your store) from the people who care enough about their network needs to think a good wi-fi connection is worth something.

Essentially, it's a defensive maneuver.