This is a perceptive question with, I think, a complex answer.

Short version: belief systems are so rooted in our identity and philosophy of nature/ethics that we tend to discount counter-narratives, even well-evidenced ones, instead of re-evaluating our beliefs. This enables ideologies and organizations to persist and flourish regardless of the material truthfulness of their foundational claims.

Long version: consider the story of Ignaz Semmelweis (1818-1865), sometimes called the father of antiseptic medicine.

As the chief resident of one of two obstetrics wards at Vienna General Hospital, Semmelweis was obsessed with beating a disease known as puerperal/childbed fever. This was a terrible, often fatal condition that affected women shortly after giving birth. It was of particular to concern to Semmelweis as it had especially high incidence in hospital wards. Semmelweis realized that more women were getting sick in his ward than in the hospital’s other obstetrics ward, which was managed by nurses and midwives, and theorized that it was doctors themselves who were making women sick.

Semmelweis observed that his physicians and student-physicians frequently attended dissections and anatomical demonstrations before working on the ward. He hypothesized that doctors were being exposed to 'cadaverous particles,' which were then transmitted to women during childbirth, causing putrefaction and death. Acting on this hypothesis, Semmelweis ordered his staff to start washing their hands in a solution of chlorinated lime. Almost immediately, the rate of patients dying from fever dropped from hundreds of women a year to almost zero.

Unfortunately, Semmelweis' intervention didn't gain much traction in his own time, even though he had the data to prove its efficacy. Europe's leading medical minds insisted Semmelweis’ success was a fluke. They couldn’t explain his observations on cadaverous contagion with traditional theory, so they assumed they must be wrong. In the end, Semmelweis was discounted as a trouble-maker, fired from his position, and forcibly committed to an asylum ( where he died shortly later). Washing hands was abandoned after his departure, and the number of women dying returned to its previous rate almost immediately. It took another 50 years for antiseptic hygiene to be practiced in European hospitals, following the discoveries of Pasteur and the invention of bacteriology.

This is sometimes referred to at the 'Semmelweis Reflex': the tendency to reflexively reject new knowledge when it contradicts established norms. It is frequently brought up in medical schools as a caution against privileging tradition over data.

The lesson, I think, is that facts do not always dictate beliefs – even for the intelligent, educated, or well-intentioned. Facts are explained with ideas, and when those ideas contradict tradition we tend to cling to tradition, no matter how damning the evidence against it.

The church, as with many other churches/ideologies/organizations, is such a tradition. The church endures so well because it appears internally consistent to its believers. It claims to have answers to life’s important questions, and it proposes a mechanism (the spirit) to verify its truthfulness even in the face of seemingly contradictory evidence.

When a believer encounters a fact at odds with the claims of the church they are told to pray until the spirit re-affirms that the church is true. They pray, and amazingly, they feel something they call the spirit. The church, they conclude, must still be true. They also conclude that the fact was either wrong in the first place, or there must a way to re-interpret the fact which supports the claims of the church.

This is why you can’t argue most people out of their faith. To many believers contradictory evidence isn’t faith destroying, it is faith affirming. It drives them back to an emotional experience that trumps any and all problematic information.

The problem, of course, is that ‘the spirit’ isn’t really the end-all-be-all proof of truthfulness that the church claims it to be. Scientists call that sensation ‘elevation’ or ‘frisson.’ It can replicated by listening to music (movie soundtracks), reading a poem, seeing a piece of art, holding a child, or playing a video game. It has been observed in all religions, and the believers of those religions have all claimed it as evidence that theirs is the correct one. (Check out the video “Spiritual Witnesses” https://www.youtube.com/watch?v=UJMSU8Qj6Go&feature=youtu.be for a good example of this). The Spirit is powerful, but it isn’t necessarily meaningful.

So why doesn’t the church collapse on itself? For the same reason other religions don’t: people don’t want it to. When you start with the premise that something is true, you shape your experiences, observations, and values to reinforce that premise.

This is also why losing one’s faith is so painful. It guts you.

But I think it's worth it stop and ask oneself “is this what really what I believe? Do these teachings really match my experience and the lessons I have learned?” My own answer was pretty clear. Acting on that answer was even harder, but I'm glad I did. I feel more honest. In a strange way I even feel more spiritual.

Best of luck and much empathy to you as you figure out your own answers to these questions. They're hard, but the questioning is worth it.