Change the bus colour to brown or something, since no subway lines on a TTC map would be brown and then use red for a line.
This change-over could be combined by re-colouring routes based on type (similar to what Ottawa has). Ottawa colours their route based on type, such as Local, Transitway, Express, Peak-Period, Special. Seeing as how at most subway stations each route has their own sign and gate anyway, you can different colours to represent different types of routes, at least that way colour for surface routes would have some meaning.
And I agree with the suggestion that the surface routes should use colours that wouldn't be used for rapid transit routes. We pretty much know which future rapid transit routes there will be (DRL, Finch, Don Mills, Jane, Waterfront), so reserve colours for them now, and then use the left-overs for surface transit.