That's a strawman version of naturalism. My version is pantheistic, which means only that I marvel at the properties that emerge in nature as constructions, some of which--consciousness, intelligence, autonomy, creativity--amount to personhood. So no, atheists don't have to regard people as mere "bags of chemicals." The wonder is that nature evolved and complexified living things, with no intelligent plan. Organisms have some degree of autonomy and thus aren't just machines or slaves, although animals are so relative to people.