Why do we say at six o'clock, on Monday, in 1996? Is there a deeper logic here than simply "that's how the English language works?"
Actually, the metaphors are all coherent, so there is a logic to it.
As Colin explained in his comment, and as discussed in this post,
- Months and larger measures are Containers -- 3-Dimensional: in 1949, in June, in this century
- Days are Surfaces -- 2-Dimensional: on Thursday, on Thanksgiving, on this occasion
- Smaller measures are Points on a 1-Dimensional line: at noon, at 12:03:45, at the moment
The smaller the unit of time, the fewer dimensions. Just a map location - at Exit 37, at 2:33 pm.
The bigger it is, the more experience it represents. A day is a page of events -- it's flat, whence on. Anything bigger than one day has to be able to stack the day pages, so it's a volume, whence in.
Metaphors always have an internal logic.