There is what I think of as the Cynical Reading of Early Modern philosophers, notably Descartes and Spinoza but the claim extends to every 17th and 18th century philosopher who discusses God (with the exception of Berkeley who is clearly in earnest, and whose reasoning for the existence of God is quite original and unique, whatever its other merits). The Cynical Reading claims that Early Modern philosophers are closet secularists who affirm the existence of God so as to not get into trouble with the authorities and, more importantly, to make the new science of nature palatable for the popular culture. For example Spinoza, on this interpretation, identifies God with nature in order that we can simply get on with studying nature, the "intellectual love of God" (similarly Newton famously remarked that in explicating the mathematical constants of nature he was "revealing the face of God"), much as Berkeley, concluding that Locke's account of "extended substance" vs. perceptions was hopelessly muddled, proposed that we simply ditch extended substance altogether and start over with perceptions only.
I don't think that the Cynical Reading is coherent. Even Leibniz, who did in fact have a public philosophy and a gnostic philosophy, continues to discuss God in the gnostic writings. Newton, for that matter, hid the extent of his religious convictions, which were intense, rather than the other way around. Even Hobbes, who has an austere materialist metaphysics of "matter in motion," devotes the second part of Leviathan to a (to my eye very murky) discussion of religion. The only Early Modern who is patently and outspokenly atheist is Hume but he appears to be quite sincere in this after all. And when Nietzsche dismisses Kant's "noumenal" world as simply a place to store God now that He is banished from the natural ("phenomenal") world Nietzsche is accusing Kant of fooling himself, not us.
I think that there is a more interesting response to the Cynical Reading than just appealing to textual evidence that the Early Moderns were sincere. The problem with the Cynical Reading of the Early Moderns is that it requires the proposition that philosophers of the 17th and 18th centuries had already absorbed the secularist implications of the new science, and sat down to write their works after some prior process of coming to understanding. And when did this difficult process occur, since we have no record of it? No, these people may be investing the term "God" with some technical meanings (Spinoza, Leibniz), but when we read these texts we are looking at the process of moving from the old faith-based epistemology to the new science-based epistemology. This is a transitional period (part of what accounts for the incredible philosophical richness of the relatively short historical period from Descartes' Discourse to Kant's Critique), and what we see in these discussions of God is the process itself unfolding. The Early Moderns are both theologians and naturalists, these conceptual systems cohabiting the same heads, an historical condition fraught with difficulty, and that very difficulty is driving the process of philosophical creation. The Cynical Reading's worst fault is its mediocrity: a facile reading that avoids the real issues.