The semantics of prepositions is notoriously difficult and their uses are very idiosyncratic. Their rules of use often depend on which particular ontological domain your noun phrase is in and are heavily contingent on how we conceptualize that domain and what metaphors we employ when thinking about that domain. In this case, we're talking about temporal entities like hours, days, and months.
Here are some simple rules of thumb regarding the prepositions on and at:
- Something about the semantics of "on" involves or suggests a two-dimensional entity (a surface).
- Something about the semantics of "at" involves or suggests a zero-dimensional entity (a point or precise location).
See @John Lawler's answer here where he quotes Fillmore (1971):
The preposition at is said to ascribe no particular dimensionality to
the referent of its associated noun; the preposition on is said to
ascribe to the referent of its head noun the property of being a line
or a surface; and the preposition in is said to ascribe to the
referent of its head noun the notion of a bounded two-dimensional or
three-dimensional space.
With this in mind, let's turn to temporal phrases like "on January 1, 2016", "in December", and "at 5:00 pm".
A larger temporal interval like a day is (for whatever mysterious psychological reasons) conceptualized as a surface, thus giving rise to the use of the preposition on.
Months, on the other hand, seem to be associated with containers (again, for mysterious psychological reasons), giving rise to the use of proposition in.
Smaller discrete temporal units like, for example, 5:00 pm, are naturally conceptualized as locations, giving rise to the use of the preposition at.
The mysterious psychological reasons that I appealed to above have to do with the way we represent time to ourselves metaphorically. Which metaphors we employ may have to do with how we've historically represented temporal entities: graphically with calendars, clocks, etc. But I know of nobody who has tried to carry out such a genealogy of temporal metaphor.