Quote Originally Posted by translations.nm.ru
I think that instrumental case can only be used if you are speaking about using a conventional method of transportation rather than an individual vehicle, aircraft, train, etc.

Hence, we can say "поехать поездом" meaning "to go by rail." You can say "Поехать автобусом" if you are talking about using a public bus line, but if someone owned the bus in question, he or she would be more likely to say "я поеду на автобусе (а не на грузовике)".
I would imagine that if there was a regular transportation route served by cars instead of buses, people would start saying "поехать машиной".
Эта теория, кажется, всё расставляет на свои места. Класс!