The human brain is not a monolith, but a complex multi-layered organ that has built new functions on top of much older ones ever since nervous systems evolved in ancient wormlike creatures. New, more advanced cognitive processes do not eliminate the heritage ones, but simply operate on top of them the way that continents crystallize out of the magma ocean and drift above it. Somewhere along the line, our intuition became insufficient for the amount of data our brains were processing, and new conceptual forms emerged - "answers" to questions that previously could not even have been articulated. But these were not actual answers - rather, they were defaults in the absence of answers: Catchall buckets where dreams, delusions, drug- and altitude-induced hallucinations, children's stories, fears, and hopes took the place of more immediate information sources. Thus religion was born.
But human evolution never stops, and our brains are always changing. We can never know for certain, but it's entirely possible that a few millennia before the advent of philosophy, humans may not even have been physically capable of grasping the symbolic logic required to organize the universe into logical relationships beyond the knowledge given by tradition-based skills and folklore. Rather, they may have seen everything in terms of seamless, blended transitions, and any spark of rational inquiry could only have been answered through extrapolations of that mystical sensibility.
In other words, the "God of the Gaps" exists not only in the chasm of unanswered questions, but in the personal divide between what is and what any given individual is capable of understanding. Originally, we had neither questions nor answers. Then we had questions, but no answers. Now we have answers to pretty much every question that a layman is capable of articulating (that doesn't contain an inherent logical fallacy), but the population is sharply divided in their ability to understand and make use of those answers. The fact that science has answered the question of human origins, to cite one example, does not mean that everyone is mentally or emotionally capable of processing the answer. It takes the ability to inwardly grasp scales of time and change that are truly staggering, and by implication to put one's self in perspective - neither of which is psychologically commonplace.
Although I don't want to put too fine a point on it, since it's obviously a matter of interpretation, we may be seeing an evolutionary division of mankind into those who are capable of moving forward vs. those who will always be lost in dreamland. If so, it's nothing new - like all evolution, just an ongoing process. Science has moved far beyond the questions that religion still concerns itself with, and (in a delicious bit of irony) religious minds have simply been "left behind" by the progress of civilization. They carelessly use and abuse the toys science delivers to them as technological end-products, but are incapable of absorbing its wisdom or even conceding its underlying assumptions despite the empirical verification all around them.
Over the longest of terms, I think it speaks to one part of civilization headed toward greater achievements, and another headed back to the caves - or at least to being exploited by the ethically corrupt among the former group. In other words, I think - and history backs me up on this - religion is perpetually doomed to be owned and operated by people who don't believe in it at all, or at best have a vague commitment to it that is subordinate to ambition and love of power. Such people are the only ones with both the mental acumen to control religious minds and the moral bankruptcy to use it - the religious themselves are constantly blundering into their own irrelevancy and destruction, and wiser minds know better than to believe they can manipulate sheep into being intelligent.
The conduct of religious figures throughout history and into the present bespeaks a mentality that is clearly the easiest of all to corrupt, manipulate, and pervert into an instrument of violence, greed, and oppression. It has a flawed, poorly-equipped psychological immune system that filters out useful information - things like reality - while perpetuating unhelpful beliefs and behavior patterns they've been conditioned since childhood to identify with righteousness and community solidarity. As a result, they'll never be more than they are - just medieval communities intruding into modern time, and kept in check only by rational (although not necessarily moral) political states.
But this is a dangerous state of affairs nonetheless, to have anywhere from a third to a half of humankind descending into a state of imperviousness to reason while the other half pursues science and technology to ever more profound degrees. And the danger isn't even in the religious part, but in the boundary between it and progressive civilization - a boundary where odd psychological mixtures can occur. You can get people who are fanatically religious and yet possessed of terrifying degrees of instrumental intelligence - both political cunning and a full capacity to understand and use technology to its most destructive potential. The common power-mongers among them will always be sabotaging themselves because they don't understand demographics, just as technocratic evil tends to undermine itself because it never quite grasps how individual human beings work. But every once in a while a villain comes along who understands both, and harnesses them to an agenda of pure malice - and over the centuries, the depths to which that malice can reach has somehow accelerated downward.
The further removed from civilization the religious mentality becomes, the darker its views of humankind have become - and the more ethereal and dizzying the height of scientific potential, the more dreadful its implications become when someone from the former group is capable of wielding it without absorbing its lessons. We find that we in the sane world are increasingly reduced to the role of babysitters or zookeepers in managing the insanity of the hyper-religious, and dreading the Planet of The Apes day when some apocalyptic nutjob is cunning enough to deceive the Old Money conservative establishment - a highly rational, albeit villainous institution - into giving him real power.
We know that such people will inevitably come to power: Every election where this problem festers is a roll of the dice, and eventually we're going to come up Snake Eyes. Some day there will be the most dangerous possible Republican candidate, an inconvenient set of circumstances, and a Democratic opponent who is not up to the task, and from that day for years the tools of reason will be unleashed to wreak horrors on the world on behalf of madness. The latent destructiveness of the fundie minority will be activated and unleashed on the world by some leader who is capable of intelligently managing a religious dictatorship. There are no easy answers to preventing that, although education and refusing to tolerate willful ignorance are a good start.
Science, however, is not a religion, and can never be a religion - it doesn't answer in order to end questioning, but to multiply questions and blaze a trail forward that does not end. And those who want to end questioning are abdicating the greatest gift of being human. People who need simple, thought-terminating answers and need them now cannot be reconciled to science, and the failure is not on the part of science - it is the failure of those people to grow up, to care what is true, and to understand the wisdom offered by scientific knowledge. That isn't to say there aren't plenty of otherwise rational, wise people who hold some benign irrational beliefs - simply believing in God doesn't make you part of the problem, as long as you understand that your belief is essentially on the same level as Santa Claus (another entity whose existence cannot be disproven) - but those who take it a step further and put their beliefs into an institutional format are at very least contributing to the problem.
Religion is today a solution in search of a problem, much like the human appendix - it's a tool not only inferior to the alternative, but not even any real competition. Religious psychology is an "answer" to the human condition the way that leeches are an answer to illness - in other words, not. It can survive only by stopping you from exercising your gifts as a sentient being, corrupting children to not think, not question, not see so they can become obedient adults who robotically promote the same set of memes they were originally programmed with. And here we see another cosmic irony, because when you look at the big picture, religion is a form of abortion - quite possibly the most monstrous imaginable. It seeks out minds at their youngest and most vulnerable, and teaches them to be something other than minds - teaches them to not see the world, to not probe outward with their reason and imagination, and to not evolve beyond what they receive. In other words, it teaches them to die.
So as long as there are people on this Earth who think, reason, inquire, and explore; as long as there are people who have the wisdom of science, and not just the toys it makes possible; as long as there are people who see the endless possibilities, and the Road Without End that makes life such an adventure; as long as there are people who live when they are told to die, open their eyes when they are told to go to sleep, and flow with the uncontainable passion of a being that always yearns to experience more; then conservatives are correct that there is a "War on Religion." Life itself is a war on religion, and I'm happy to be a soldier in good standing in its army.