It depends on whether you can stand up or are seated outside when being carried by a typical example of the transport in question, on its size, and if it is enclosed.
Cars and the typical small helicopter typically don't really allow a person to stand up and are enclosed, therefore one is "in" them.
On the other hand, early open-cockpit aircraft and later passenger aircraft, buses, bicycles, motorbikes and ships all allow their users/occupants to stand (or the occupants are seated outside), hence one is "on" such transport.
Small boats are a mixed case; One can be "in" or "on" a small, boat. On the one hand it is small and may be enclosed, on the other hand, one can stand when aboard one (however foolish it may or may not be to do so), and one is seated outside when sitting.
If we have an imaginary vehicle, eg a "snarfblagger", if it is small, enclosed, and doesn't really allow a person to stand within it, a person using it is probably "in" it. On the other hand, if the "snarfblagger" is ridden like a bicycle or a horse, or is large enough to stand and walk around inside, then a person using it is "on" it.