"mit [mode of transport] fahren/fliegen" implies that the speaker/subject isn't necessarily the driver/captain. This is best translated by "take the [mode of transport]".
mit dem Bus fahren
mit dem Auto fahren
mit dem Motorrad fahren
mit dem Schiff fahren
mit dem Flugzeug fliegen
As far as "Mit welchen Autos fahren wir?" goes, think of a group of people setting up a carpool. They have more cars than they need and the speaker is asking "Which cars shall we take?".
No, in German the "mit" is necessary, otherwise the question makes no sense. I even think it is necessary in English, in order for the question to have the same meaning... it should be With which cars are we driving? or Which cars are we driving with? (in the sense of "Which car are we taking?")
"Which cars are we driving?" should be translated as "Welche Autos fahren wir?" which has a slightly different meaning to me.
Thanks. The German distinction makes sense. In English, though, I think you'd say "which cars are we taking?" (assuming a car pool).
You wouldn't use "with" quite this way . . . "with which cars are we driving?" would only make sense if there were a couple of groups of cars, and you weren't sure which group you, yourself, would join with your own car.