The story of the first revelation is just a story without any evidence. Also there’s no credible evidence to establish whether or not prophet Muhammad AS was literate. There are some narrations that lead us to believe that he could at least read, but nothing can be said with certainty.
As for your question regarding why it has been interpreted as ‘read’ for so many years – evidently it is because all these years Quran was not a focus of the scholars. They were more interested in other fields such as jurisprudence, philosophy, tassawuf/mysticism, etc. Besides this kind of errors do happen in other fields as well. A classic example that can be used is Aristotle’s concept of this universe which was completely rejected by Einstein just recently in favor of an entirely opposing concept.