The public transportion in Chicago is a joke compared to San Francisco? The Blue Line and the Red Line run 24/7, and connect most of the city. The only cities of comparable size with better public transportion are NYC and DC.
All I've taken in SF is BART which was a better experience than the El. Also, the spoke model makes it a lot harder (but less confusing I suppose) than the NYC or Parisian model to get from point a to point b without having to detour through downtown.
Big swaths of San Francisco aren't reachable from BART. It's not comparable to the CTA, or the MTA, or DC Metro Rail.
If you include MUNI light rail in the picture (it does add another ticket/payment to the trip) then SF is covered much better than Chicago. The El is not bad, but the fact that you have to go down to the loop to get anywhere is a major PITA.
Much of the coverage you're talking about is essentially bus coverage, isn't it? Are we really comparing trollybusses with trains? Chicago is saturated with busses, but I wouldn't know how good they are, because nobody I know lives somewhere where you have to take a bus.
"safest big American city I've been in."
As a life-long Chicagoan I still find it incredibly strange that people believe Chicago is safe. It has a very high crime rate, double NYC in every category.
The climate may suck, the public transportation a joke, the government corrupt as hell, but doggone it, it's clean!