No one is too sure about this, although many speak with imagined authority. The folk etymology of the phrase/practice is that this refers to a pagan cult where the plaintive asks for protection from ancient tree spirits; while a Christian overlay is that the practice similarly refers to the wood of the True Cross.

This site does a good job of describing the possibilities. I'm always a bit skeptical of historians who assert that "oldest reference" equals "point of origin." Folk practices frequently predate the oldest reference, so the question is usually by how much. It is of interest that the oldest references to the practice are in the nineteenth century. The site notes - with the good authority of British folklorist Steve Roud - that there is significance in a nineteenth-century children's game similar to "tag" in which "touching wood" made one "safe." This may be the origin of the practice, but being certain is not possible.