This may be counterintuitive, but: there is no guarantee that a real-life transit system will reduce traffic congestion. This is due to the induced travel effect.
Congestion is an sign of equilibrium between number of people who want to travel and the amount of mobility available to them. If you provide more mobility by improving public transportation, or by adding more lanes to roads, then the equilibrium will settle at a new level with more people travelling. There will still be congestion and delay, but more people will be able to get around.
Read more about it: the
Downs-Thomson paradox, the
Lewis-Mogridge position, and articles about
induced demand.
Note that this effect only applies where there are sufficient numbers of people to provide a source of nearly limitless demand on transportation: for example, to a city center. But the idea is really simple. If so many people switch from roads to rail (for example), then the roads will become improved to the point where they attract people back onto them, until it gets congested again. Equilibrium.
So in the game, if you do some kind of traffic reduction due to existence of public transport, then it is an artificial factor. Ideally, you should simply model desire to get from source to destination by the best mode, and let it play out. You should also consider destination parking availability as a significant factor in choice of car mode (this isn't explicitly modeled in the game AFAIK). If the player is actually able to exhaustively satisfy the population's demand for transportation service along certain segments, then you'll see traffic congestion thin out there. But either way, providing enhanced transportation links will allow larger and larger numbers of people to travel regardless of the level of congestion. And that's what (grade-separated) transit provides.