Daniel Garber is not only a professor of philosophy, at Princeton, no less, but he actually specializes in philosophers of the 17th century, and he says things like:
"Many important scientists and mathematicians in the period were also believers, including Bacon, Descartes, Boyle, Pascal and Newton. Not that there weren’t atheists in the period"
Professors of philosophy have often been roundly mocked by actual philosophers, and with good reason. Yes, Pascal and Newton believed in God. With Bacon and Descartes, there is a lot to read between the lines, just as there is with Hobbes and Spinoza. I assume that the latter two may be among the people Garber counts as atheists, but they didn't come right out and say they were. Not even David Hume, born decades after both Spinoza and Hobbes had died, did that. It would've been extremely dangerous.
The first open, public avowal of atheism in Europe after the 5th century of which I am aware is contained in the book Système de la Nature ou Des Loix du Monde Physique et du Monde Moral, written by Paul Henri Thiry, Baron d'Holbach,
and published in 1770. Published, but under a pseudonym. And it was banned in France, and an executioner publicly burned some copies of it. Was Holbach himself in danger of being burned at the stake? Probably not, but the treatment of his book probably reflected what some of the authorities would've liked to have done to him. Diderot, not an aristocrat like Holbach, spent some time in prison in the mid-18th century in France for atheism expressed between the lines. (The Marquis de Sade spent some time in prison for his writing, and Marquis is a few ranks above baron, but Sade's writings are many shades more shocking than Holcach's. In case you haven't read any of Sade's work, and you have read some Penthouse Letters, imagine writing which might make a Penthouse Letters editor cringe in horror and scream, "That's sick! It's wrong! I want nothing to do with such filth!" and burst into tears like a little girl. I'm telling you, Sade was an uninhibited writer.)
Jean Meslier, 1664-1729, was a French priest, and after his death a strongly-worded essay in favor of atheism was found among his papers. So that may be an actual written smoking-gun, no-doubt proof of 17th century atheism -- or maybe not, maybe Meslier didn't lose his faith until after 1700. In any case, he, like many other clergypeople in the 18th and 19th centuries, when atheism gradually emerged and asserted its right to be, demonstrates that how one could be publicly religious and privately atheist. Descartes, whom Garber counts among the religious believers of the 17th century, was often thought by his contemporaries to have been an atheist, as was his follower Spinoza, and whether they were atheists or not, they certainly paved the way for later generations to say openly that they didn't believe in God, without fearing punishment for it. As did Francis Bacon and Hobbes and Hume and Holbach and Diderot and Sade and Voltaire and Franklin, because they all pushed the boundaries of what was permissible to say. They all stuck their necks way out for the sake of the freedom of expression of the likes of you, me, and Garber.
It's soooooo absurd to make sweeping generalizations about the religious beliefs of people who were subject to punishments up to and including torture and being burned alive for religious dissent. Both Garber and I are, of necessity, reading between the lines when it comes to the religious beliefs or lack thereof of 17th century philosophers. But only one of us acts as if he is and admits how much guesswork the subject involves.