I don't know about SF in particular, but for major downtowns "just trying to pass through" just isn't being done in peak hours (when congestion matters the most

I don't know about SF in particular, but for major downtowns "just trying to pass through" just isn't being done in peak hours (when congestion matters the most), the peak traffic consists from the daily commutes to/from work, so the whole point of downtown congestion pricing generally is to push people who commute to their work by car towards some other means of transport. Of coarse, there needs to be some reasonable alternative, otherwise that's meaningless as an incentive.