"I'm going to go to the bookstore IN Kyoto." "at Kyoto" doesn't work here.
Here are some general ideas for using IN, AT, and ON for places, but they aren't useful all of the time.
IN = for the "larger, more general places" a country, a city, a neighborhood
I live in Kyoto
AT = for the "specific, more exact information about the place" a specific building, the specific address, etc.
I am at the bookstore.
I live at home with my parents.
I live at 2020 Main St.
I'm at the door. Please let me in!
(BUT! I live IN apartment 2C.)
(BUT! It's located IN the center of the city.)
ON = "places that are not too general or too specific, or a wide flat area
I live on Main Street. (no number)
on the avenue
on the boulevard
It's located on "the green line" (when you talk about a subway line).
I live on a farm.
The building is on the plaza.
ON = public transportation = you and strangers riding together
on the bus
on the plane
on the subway
on the train
and....on a bike (because you sit ON it)
IN = you don't just "walk onto" it.
in the taxi
in the car
There are only about 5000 exceptions to these "rules".. : ) You have to know if you are located there or going there too!