The methodological naturalist doesn't address the big questions in metaphysical terms, but she does so in pragmatic ones. She bars supernatural explanations at the outset because they're unscientific. On pragmatic, methodological grounds, she doesn't appeal to miracles or gods. Thus, effectively, in her professional capacities as a scientist, she's an atheist.

She can be religious in her personal life only by living with a split personality. She must reconcile her personal beliefs with her professional assumptions, by resorting to specious excuses for her religion's creed and scriptures. While she's being scientific, she must treat her religion as though it were nonsensical.

As far as scientists are concerned, nature as such is godless. Scientists objectify nature, leaving no room for a foundational subjects. Scientific methods, therefore, are effectively atheistic.