Francis Bacon was no atheist; he sought to tread the via media of the reformed English church between the two extremes of Popish superstition on the one hand and profane superstition on the other.
In his Meditationes Sacrae, in the section titled “Of Heresies,” Bacon writes:
Ye err, not knowing the Scriptures nor the power of God (Matthew XXII:29)
THIS canon is the mother of all canons against heresy: the causes of error are two; the ignorance of the will of God, and the ignorance or not sufficient consideration of his power; the will of God is more revealed by the Scriptures, and therefore the precept is, “Search the Scriptures;” the will of God is more revealed by the creatures, and therefore the precept is, ” Behold and consider the creatures:” so is the fulness of the power of God to be affirmed, as we make no imputation to his will; so is the goodness of the will of God to be affirmed, as we make no derogation from his power: therefore true religion seated in the mean betwixt superstition, with superstitious heresies on the one side, and atheism with profane heresies on the other; superstition, rejecting the light of the Scriptures, and giving itself over to ungrounded traditions, and writings doubtful and not canonical, or to new revelations, or to untrue interpretations of the Scriptures, themselves do forge and dream many things of the will of God, which are strange and far distant from the true sense of the Scriptures; but atheism and theomachy rebelleth and mutinieth against the power of God, giving no faith to his word which revealeth his will, upon a discredit and unbelief of his power to whom all things are possible.
In placing the Anglican church between the two extremes, Bacon is borrowing from Aristotle concept of virtue flanked by its two respective vices. He does this even as he is busy replacing Aristotle with his own inductive method for discovering the hidden truths of nature.