Well, I can't answer why, because there is no logic to it. But I can give you some examples.
I am at my desk. I'm sitting in a chair.
I am at my desk. I'm sitting on a chair.
(Both are correct).
My friend was sitting in his wheelchair when I arrived.
(not on his wheelchair)
I thought he would be in bed, because he had told me he was ill. I went to his bedroom first, and all I saw was his robe, which was on his bed. He was downstairs having breakfast on the balcony.
(not in the balcony)
Also, I'd like to add that a person sits:
on a bench, on a stool, on a couch/sofa
in bed (if under the blanket), on the bed (if not under the blanket), in the bathtub (if in the water), on the bathtub (if on the edge of the bathtub) in the bathroom, in an easy chair, at a desk, at a table
on the toilet, on the floor, on the grass, on the tennis court, on the deck, on the roof
in the garden, in the basement, in the attic, in the kitchen/office/living room, etc.