I had the same thought when reading the article. NYC became NYC partly because of the need for physical proximity of businesses. For example, there was a time when you HAD to be physically present on Wall Street to exchange stocks.
In the 21st century, how great the need for physical proximity in the tech industry? Sure, it's convenient to have a ton of skilled devs in one place, but does that convenience outweigh the (rather extreme) cost? Is this sort of flocking behavior a cultural hand-me-down from a bygone area?
That said, this isn't an either/or situation. We can fix SF's mass transit situation AND we can find ways of spreading out businesses across the US.