My hypothesis basically goes like this:
1. The Stormfather is some sort of spren or spren-like being that is separate from Jezrien, the Herald.
2. When the Radiants were formed, the Windrunners learned from their honorspren about the leader of the honorspren, known as the Stormfather.
3. Someone in the Windrunners jokingly started to refer to Jezrien as "Stormfather" because he was their leader, and the name stuck .
4. Over several desolations (and the associated knowledge loss) and the 4000 years since the last one, people who heard the Windrunners calling Jezrien "Stormfather" started to believe he really was the Stormfather, helped by the fact that they never see the real one and/or Jezrien being awesome enough with his powers that it was believable .
There is basically no real evidence for this, but I think it a believable hypothesis for how Jezrien might become know as the Stormfather and worshipped as such when he isn't.
There you go, rip it apart if you wish .