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.
ell.stackexchange.com/users/5283/Monty Wild
Here's a jumble of thoughts, because I'm not sure if there is a definitive answer here:
I believe you would use "on" in any situation where you could ever describe yourself as "boarding the [vehicle]".
You can use the verb "to board" with train, plane, or boat.
Once you have boarded the plane, you are on board the plane - or just "on the plane" for short.
You would not board a car, though.
Also, to be "on the car" would mean to be sitting on the roof of the car - so perhaps we do not use "on" with "car" because it would have a different meaning than the one we intend.
You can board a helicopter, and
I think you could therefore say "on the helicopter", though I think more people would say "in the helicopter".
[Maybe this is because being "on" the helicopter, as with the car in the above point, would be extremely painful if the rotor were moving :P]
ell.stackexchange.com/users/123/hairboat
You get on a train because you can move around from car to car and walk around from place to place, you get in a car because you must remain seated in a single position inside the car and do not have the option of moving around.
ell.stackexchange.com/users/5284/anonymous
I think you're right in saying it is involved with the size and the nature of the vehicle.
I have no history to back me up here, but I believe it goes like this: You cannot physically get on top of a train in any normal environment.
You stand on a platform and then you get onto a train.
It may have originated from the days before platforms, where you would climb up to reach the train, thus getting 'on' it.
This is similar with both buses and boats.
You tend not to get on the roof of one.
You also tend to stand on buses and trains, and may consider the floor of the vehicle as what you stand 'on'.
A car is different.
They're not all that big, so standing on one is different to being in one.
You don't stand up in cars.
You always consider being in a seat instead of on a platform.
A car is smaller, so you feel more claustrophobic, and definitely inside .
ell.stackexchange.com/users/4587/MMJZ
It's because of the location of the thing that moves the vehicle, the size of the vehicle, and its height.
On a train, the tracks are below you, and you typically must use a small set of steps to climb up to the height where the people and cargo are. "
In" also works for a train, but it isn't as common because a train is very large.
In a helicopter, the rotor blades are above you, and the vehicle is typically quite small with a very small payload capability, comparable to a car.
On a jet or in a jet both work.
On bus, in a bus both work.
For most road vehicles, only the biggest ones work with "on", like buses.
In a boat and on a boat both work, but "in" is more commonly used for very small boats, and "on" is more commonly used for big boats.
ell.stackexchange.com/users/5287/badon
I don't think it's particularly strange or illogical if you think about it.
Like others have mentioned it implies nuances regarding the subject vehicle.
With a car being a small motor vehicle
the in implies the movement of lowering your arse to the seat immediately as you enter.
A train or bus being larger vehicles require the patron to step on to a platform or step through the doors first before taking a seat.
The same applies to ships, planes and trams.
This is the same with board as in to board a train I presume
you know it's not usual to board a car .
ell.stackexchange.com/users/5302/Lee
I was trying to work out why get  in  car but  on  most other transportation systems.  Get in  a car, helicopter  Get on  a train, plane, boat (although  in  feels like it works ok here)  Is it the size of vehicle? The function (private/public transport), or something else? How would you know whether to use  in  or  on  for an unknown vehicle?
Why do you "get in a car" but "get on a train"
ell.stackexchange.com
<word-usage>
ell.stackexchange.com/questions/19761
ell.stackexchange.com/users/5280/RichK
You get on a train because you can move around from car to car and walk around from place to place, you get in a car because you must remain seated in a single position inside the car and do not have the option of moving around. It depends on the size and the nature of the vehicle. You would use "on" in any situation where you could ever describe yourself as "boarding the [vehicle]". On' is used in any boarding situation. Otherwise this depends on the size and nature of the vehicle.
On' is used in any boarding situation. Otherwise this depends on the size and nature of the vehicle.