A method of making a heat treated (HT) substantially transparent coated article to be used in shower door applications, window applications, tabletop applications, or any other suitable applications. Certain embodiments relate to a method of making a coated article including heat treating a glass substrate coated with at least layer of or including carbon (e.g., diamond-like carbon (DLC)) and an overlying protective film thereon. The protective film may be of or include both (a) an oxygen blocking or barrier layer, and (b) a release layer of or including zinc oxynitride (e.g., ZnOxNz). Following and/or during heat treatment (e.g., thermal tempering, or the like) the protective film may be entirely or partially removed.