That confusion is often blamed on Protestants. But it’s more accurate to blame it on humanists and others of the early Renaissance, who wanted to bask in their rebirth of civilization after the awful period of the Middle/Dark Ages.
They were so in love with the classical world that they were unable to see any of the good things achieved during the interim. Which were many.
I take your point, but I think it is just as likely that the confusion is a confusion of the mind brought on by imprecise definition. The Dark Ages; the Middle Ages; the Medieval Era; The Age of Discovery; The Renaissance; all refer to specific events and times, but these events and times seem to have conflicting boundaries that impinge on and clash with one another.
It seems to be a feature of human action that our behavior cannot always be so conveniently compartmentalized as to fit so precisely that it always can be kept in neatly defined spheres.
This is true, I think, even in the broadest categories of human action over great historical eras.