Some transport uses ‘in’. Some transport uses ‘on’.

The rule for this is not whether you can go inside the vehicle.

The rule is:
services use ‘on’
independent or special transport uses ‘in’

An easy way to think about this is: does the transport usually do this journey, even when I am not here?
If it does, it probably uses ‘on’.

Common Examples

I came on the train.
I met my wife on the bus.
There was a dog running around on the ferry.

He left his keys in the car.
I hate it when they show adverts in a taxi.
Every summer at the beach we used to catch crabs and let them run around in the boat.

Note: although taxis may drive around all the time, they don’t do a journey unless somebody tells them where to go. So they use ‘in’.

Comparisons

I left my phone on the bus. (OK if the bus is a normal public bus)
I left my phone in the bus. (can be used if it is a privately hired bus)

I came on the plane. (Ok for general planes)
I came in my plane.

Exceptions

Bicycles use ‘on’.
Large private boats often use ‘on’, although they can also use ‘in’. However, smaller boats are more likely to use ‘in’.

I came here on my bike.
The billionaire is always having parties on his boat.
They went out fishing in Dave’s boat.