It's a little easier in Chicago due to our more boring grid layout (Lincoln Park? I'll take the Red north and transfer to the Brown. Logan Square? I'll take a westbound bus and get on the Blue), but iOS 6 has still given me exactly the same thought of switching to Android for the transit navigation.
Totally, I was in Chicago for work earlier this summer and Apple Maps was completely useless. Luckily I still remember the transit from when I lived in Chicago a while back, but had I not had that prior knowledge I would have gotten myself lost many times.