I see a large part of the problem as being the treatment of religious texts as explaining the physical universe, while science claims to be able to derive other aspects of philosophy and morals.
Both are poor fits. When religious belief contradicts scientific explanations of real world phenomena, religion generally loses (granting that science has made its own errors).
There have been attempts to derive morality scientifically, with varying degrees of success, but most of them lack flavor and are thereby unappealing.
Science is all too often materialistic, which is every bit as faith-based as any religion. Individual experience nearly always includes elements for which no scientific explanation is readily forthcoming/
Above all, both sides claim to be close to total knowledge of the universe, which is so totally laughable as to defy any sort of discussion. Science tells us that about 96% of the universe is dark matter and dark energy, about which we know nothing, and yet claims to be close to a “unified theory of everything” — ludicrous.
Religions claim, too often, to have all the answers to everything revealed by god(s) in an age when understanding of even the basic mechanics of the universe had yet to be grasped — also ludicrous.
Both science and religion have focused at various times on insuring that they be ascendant at the center of things, as a means to power. This weakens the reputation of both as seekers after truth.
