Many philosophical problems informed my view of religion, but probably the most profound were Carl Sagan's invisible dragon and the problem that there are so many differing and incompatible religions. Many religious people will freely admit their beliefs have no evidence, and yet from my point of view, if that's true, how can anyone claim their particular religion is correct? Why should I believe in Hinduism instead of Catholicism? I never got a satisfactory answer to that in any of my philosophy classes or reading. (The problem of evil is another strong one, but didn't have as big of an impact on me as the first two.)
As far as science goes, the two main contributors to that were biology and physics (although there are some countervailing forces there: the order of the universe truly does seem miraculous). Jay Gould's essay "non-moral nature" where he describes parasites that lay their eggs on paralyzed victims, then the eggs hatch and the larvae eat the victims alive, was probably the first thing I read that had bearing on religion. But if you look at nature generally there is obviously an overwhelming amount of suffering. Kids who die from random genetic mutations, animals that get eaten alive crying. I could never square any of that with God.
As far as physics, what really gets me is the sheer immensity and seeming indifference to human scales. Because of the speed of light, we are basically trapped within our own universe. Space is mostly an enormous empty void, and there is no sign that any other planet would be especially hospitable to our species. On a more mundane level, human beings have been killed in incredibly stupid ways, like the guy who was irradiated to death because of a software bug in the x-ray machine. So you put all of that together and it just doesn't suggest any sort of divine guidance to everything going on around us. (Which isn't to say there aren't counterarguments, but that's the sort of evidence and thought processes I imagine the parent was referring to.)