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.