I think that there's one big thing that you've overlooking, and it's not a minor issue.I'm not talking about drivers as a narrow slice, I'm talking about drivers who are willing to use transit even occasionally as a narrow slice.
Traffic into Toronto is now (thought to be) so bad that people will actively try to avoid it.
I bet you that if you were to poll most daily commuters on the GO lines why they switched over, a majority of them would say that the reason why they use GO is because driving into the City has become more trouble than it is worth. Hell, there is at least one blog dedicated to just this. (http://www.thiscrazytrain.com/)
Because of this, much like @crs1026 wrote, the answer isn't simple - Metrolinx do need to continue to cater to the auto driver, and especially in the suburbs. They have no choice in the matter.
But they could also be taking steps to make the stations more accessible to everyone, and not just auto drivers. Locate the station buildings near major cross streets, and improve pedestrian and cycling access. Make access to the bus loops more streamlined, and not requiring a mile-long reroute to get to them.