SF has the worst transportation, but also has the best flow (By a hair) between downtown and neighborhoods, and as far as I know, more residential near the CBD, so if one has time it is more enjoyable to walk and is less prone to problems via the elements. So those are it's saving graces... but it ends there.
There is only one subway line though which is actually just commuter rail primarily serving the suburbs (BART) with only 8 stops in the city. only 6 of those are places you'd want to go and all linear unless you want to count Glen Park or Balboa Park. Otherwise you are stuck to taking Muni, which is the slowest transit in North America.
Not even close to a true subway system like Chicago or Toronto has. Should not even be mentioned. Chicago has about twice this many just in the 2-3 square mile Loop. I just did a count and found 55 subway stops in the "north side" area, 40 if you pretend that the loop is not there.. Not including the Metra stops which would add another 8-10 stops, or the much larger bus and taxi fleet...
"With an average vehicle speed of 8.1 mph, it is far and away the slowest major urban transit system in the nation."
The Muni Death Spiral - Page 1 - News - San Francisco - SF Weekly