I totally agree about the downsides. Even when a bus goes from exactly where I am to exactly where I want to go with no transfers or half-mile walks in the middle (which, incidentally, is almost never), I still have to conform my schedule to the bus's. If it runs every ten minutes, that's no big deal, but if they run every 40 minutes (like my school's shuttles) or every 20-60 minutes (like the CTA is wont to do), that's just not going to work.
My most frequent use of my car is a trip that takes 40 minutes through the city by car, and 2+ hours by bus/train. I would love it if the CTA managed to increase frequencies and fix all the slow zones on their track. It's just never going to happen.