The gods is a name wrongly given by Men to the Valar. While Tolkien states that Men have 'often' called the Valar gods, in fact the term is very rare in his later books; it is most prominently used at the debate of Estolad, where the Men newly arrived in Beleriand dispute whether or not to remain. This is natural, of course; they had not at this point been tutored by the Elves in such high matters.
It is tempting to suppose that 'Men have often called them gods' refers to the years after the end of the Third Age, and might even suggest equivalences between the Valar and mythological gods of later times, such as those of the Greeks or Vikings. This cannot be correct, however; the Valaquenta represents a very ancient text within the context of The Silmarillion, probably dating from the mid to late First Age, and therefore can only refer to the Men of those times.