Perhaps including GO into the regional transit authorities' express fares could work. For example, with the TTC it costs an extra $2.65 on top of your current fare to take the downtown express buses. In York Region to take 407 express buses (and perhaps express branches of other routes, not too sure) it costs an extra 50 cents on top of the current fare. Essentially make these fares the cost to ride GO services within a specific zone.
Perhaps we should also consider these fares for all day limited-stop lines as well, such as Zum, Viva, subway, etc to help raise revenue. On the other hand, according to thebigmove.ca, increasing transit fares apparently would do little to help pay for transit.