Originally meant
From English thumb, the body-part name, in the older concrete sense of using the thumb's breadth as a rough measuring standard; the phrase developed from the idea of estimating by that informal physical measure.
Background
The expression is recorded in English by the late 17th century, with early examples referring to rough measurement or practical workmanship. The popular link to a supposed legal right to beat a wife with a stick no thicker than a thumb is a modern folk etymology and not supported by the historical record; compare similar Germanic body-part words such as German Daumen and Dutch duim.