This was the metropolitan area, though. If you look at the chart, the top-left column states "Top 25 metropolitan areas, by population". After all, everywhere in Silicon Valley is expensive, not just SF proper. San Jose is not itself cheap.
SF isn't in Silicon Valley. San Jose is one of 10 largest cities in the county and Oakland's pretty big too. I'm guessing that "San Francisco metro area" probably can't include either of those two larger cities, nor would it include Silicon Valley (which is 15-20 miles from SF and closer to San Jose.)