I commuted from Kitchener to Toronto for work every day from September to December for co-op on the GO "Express" train. It was 2 hours each way to travel about 100km. It's just about the farthest thing I'd call from "good public transit."
If you drove that during rush hour, you wouldn't be travelling at max speed the whole time, and likely would also take two hours to travel, potentially more (Google predicts up to 2 hours and 40 minutes).
Step 2: compare to alternatives, factoring in geography, culture, scale of operations, political environment
It's a hugely complex issue. I wouldn't define Toronto's public transit as bad, but it's not world class.
The train takes 2 hours to travel 100km. Cars can do that distance in one hour, despite having to cope with traffic. That's pretty appalling. Good public transit should be faster than a car along its main corridor.
Apart from geography, those other factors are reasons, not excuses. Lots of people here look down on public transit and associate it with poor people. That's a problem to be rectified.