A Google Maps Help has one Seattle mass transit commuter asking why the transit directions are not a 100% correct. In short, the routes Google plots for some transit directions do not follow the actual routes used by that transit agency. Instead, Google will plot a straight line, and not go along the streets.
You can see an example of this by clicking here - notice the route is basically a straight line across the map. Of course, this may change if you read this article months later, but for now, this is how it works.
Google's Dave explained why this may happen. Dave said:
Currently, we rely on the transit agency to provide us with information on the route. Although transit agencies can provide us with the exact shape of their routes, not all agencies do so. So we interpolate between stops, which we think is better than showing nothing.
That makes sense but obviously it might not be too clear to those using the transit directions. So Dave added, "I'll look into whether we can do something to provide a better experience on our end."
Forum discussion at Google Maps Help.