This assumption is where the problem is. For example, Google employees live in central San Francisco but commute to work in Mountain View because a bus service was added. They wouldn't be attempting that commute in a car in the first place. These busses have added to traffic, not reduced it.
I think that's an unfounded assumption. I know plenty of people who do in fact drive daily from SF or Oakland down to MV/SJ.
Well so was the original assumption!
If none of those people would drive instead, or even if only a couple of them would, then the massive bus is a negative.
And even if all of these people lived in walking distance of where they worked, the places they've now vacated would be occupied with people who may drive, and so forth.
The imaginary world you're supposing does not exist, hence the article we're discussing to begin with.