There aren’t any simple rules per se, and most people, when asked why you use one preposition over another in a particular case, will usually give an explanation by analogy with a more simple example. But it can be hard to invent these analogies if you don’t already know which word to use.
Fortunately there is a good tool you can use when you are wondering which form to use: check for collocates using a corpus, such as the freely-available Corpus of Contemporary American English.
Using COCA, you can search for frequent prepositional collocates before a questionable phrase using
[i*], the code for prepositions. For example, if you are unsure whether you should say “in a bus” or “on a bus” you could search for
[i*] the bus, and you would get these incidence counts:
1 ON THE BUS 1444
2 OF THE BUS 792
3 TO THE BUS 414
4 OFF THE BUS 340
5 AT THE BUS 283
6 FOR THE BUS 249
7 FROM THE BUS 179
8 IN THE BUS 170
Clearly the most common prepositional collocate for “the bus” is on, although there are curiously some 170 examples of “in the bus”. So you click on them and you see:
- They were huddled in the bus shelter, out of the wind
- Flea Market 8 a.m. -3 p.m. Saturday in the bus parking lot.
- Optimism is a rare quality at 4 a.m. in the bus station in Cleveland.
So far, so good. These are examples where bus is just the beginning of a longer noun phrase to which in can be perfectly reasonably applied. But then:
- they were in the bus trying to help
- Some team members were still in the bus and we were able to get them out.
- The eight men were separated from the women in the bus, and driven away, along with their father's coffin.
- The tourists in the bus didn't seem to give a damn.
What the heck is going on here? I thought that you had to say “on the bus”, and that “in the bus” is wrong. Well, I guess sometimes you can say “in the bus”, although it seems from the contexts given that you would only use “in the bus” when the bus is stationary and can be thought of as a room or building or sorts.
Anyway, you can learn a lot about how to use in, on, and at by searching through a corpus and seeing which preposition native speakers use most frequently with the noun you are wondering about.