It seems to have something to do with whether the target location is conceived of as one-dimensional or two-dimensional, and whether we are thought to be able to penetrate the target or not. For example, we have no idea what it would mean to be "in the beach." Even if we were buried there up to our necks, we would be in the sand rather than in the beach. On the other hand, a parking lot is a broad rectangle that can include us, so we can be in it. I can put a corn chip into my mouth, but not into my smile, even if I am smiling while I am eating the corn chip.

For functional purposes, all languages just have collections of fixed expressions linking prepositions to various things and activities. At least in English we don't have to memorize accompanying changes in case endings for the nouns involved, so life is relatively easy for us.