Rent prices have everything to do with supply and demand. One of the reasons they're so high in San Francisco is that it's surrounded on three sides by water, which restricts outward supply expansion. And then zoning restricts upward supply expansion. You have much the same issue in Manhattan, which is an island.

How else do you explain housing costs being lower in Austin (available land, less restrictive zoning) than New York City despite Austin having a higher median income?