How big is Cupertino? Not that big, yes? So traversing it by car can't be more than a fraction of the time it takes to travel all the way from SF to Cupertino in the same car.
To increase efficiency, you wouldn't cart JUST Jony Ives in his own private car, of course. You'd pack in a busload of people into...well, a bus, and drive all of them at the same time. This cuts down on congestion.
A bus would be most efficient, but that is only if a bus load of Apple employees lived in the same area as Ive AND wanted to travel to and from work at the same time as Ive.
Also, for Ive to commute by train, he needs to first go from his house to the train, then get on the train, then travel from the train to work. This is not going to be faster than taking a car directly from home to work, and might take significantly longer. For you and I, it might not matter, but for a busy man like Ive, I think it does make sense to drive directly from home to work.