It's costs.
Commercial rents have skyrocketed. Moreover, residential rents have skyrocketed to the point where few people in the service industry can afford to live in SF at market rates. Even if you can find a space, how are you going to staff it? Who's willing to commute in from Oakland (which is getting expensive too) for a low wage job with grueling hours?
Nopa, one of the most successful SF restaurants in the past 10 years, is posting job ads for cooks on their menus now.
This isn't because of a slow permit process. Nopa hasn't applied for a permit in years. It's a result of the macroeconomic effects of a tech boom. So while I'm very happy to see PG highlight macroeconomic factors that foster economic growth in cities, I see a missed opportunity to fully address their complex effects.
This is probably because this issue has been politicized here in SF, with the tech industry often lambasted for "destroying" the city (this comes from a lot of the people getting pushed out), so tech folks often get hyperdefensive and contort themselves trying to point fingers elsewhere. I think that's what's happened here with PG trying to blame the government's permitting process.
But clearly if we want to continue making SF an attractive startup hub, we need to help "little restaurants and cafes" continue to open and operate. And the elephant in the room there is quite simply the high rents and high cost of living for workers in the service industry, driven by a huge influx of wealthier residents competing for space. You want a startup hub, you need city policies that manage that growth.