A method of making a heat treated (HT) coated article to be used in shower door applications, window applications, or any other suitable applications where transparent coated articles are desired. For example, certain embodiments of this invention relate to a method of making a coated article including a step of heat treating a glass substrate coated with at least a layer of or including diamond-like carbon (DLC) and an overlying protective film (e.g., of or including zinc oxide) thereon. In certain example embodiments, the protective film may be ion beam treated with at least carbon ions. It has been found that the ion beam treatment improves the shelf-life of the product prior to HT. Following and/or during heat treatment (e.g., thermal tempering, or the like), the protective film may be removed.