I think comfort with the term "gene" vs. "protein" (I agree "molecule" isn't good) depends on what biological specialty you were trained in.  In genomics, we are more likely to talk about the function of genes, not the proteins.  But to be a bit more philosophical, although the "protein" actually does all the good stuff, I think the word "gene" encompasses more of the lifespan of this "unit of heredity" than does the word "protein".  And I definitely don't want to see separate articles for genes and proteins!