No, they weren't paying their very limited staff much; it's a marginal business that's been on the decline for years, and even one of the managers is stated as having a salary of only $28k. All of this is in the article.

>managers is stated as having a salary of only $28k.

Which isn't a livable wage in SF, right? At some point businesses that can't survive cost inflation, either due to worker costs, government regulation, or energy cost must give up their space for those that can.

The manager didn't even make any money from the bookstore, it was the cafe that paid for the salary.

Not even the owner(s?) - I suspect that everyone involved including the owner could make significantly more by working even a low- to mid-range clerical job anywhere else in San Francisco.