Speaking without any references:
I’m under the impression that a lot of surnames arose from personal situations associated with people.
So you have occupations (Smith, Miller), colors, (Brown, Green), locations (Rivers, Fields), and so forth.
But what is a “Jones?” It’s a common name without an obvious (to me) origin.
Maybe it’s Spanish in origin, and it’s short for “cajones.”
OK, just kidding. Failing a satisfactory answer, my WAG is that it’s somehow a variant of John/Johns/Johnson.