Faith is part of almost everything in human life. Perhaps not faith in a divine being, but almost every person has faith in some aspect of their lives. Everyone believes in something without the critical evidence to back up their assumption. Without the ability to operate without absolute certainty then people would simply stop to function and act. People have faith in their leaders, faith in their way of life, faith in their neighbors and so on. The study of economics easily reveals how much simple belief and faith in the non-existent are required to make the global system function properly. Faith keeps people moving, keeps them pushing forward despite adversity and suffering. This is a powerful force that has done much good and bad, still is doing much good and bad in the world. Faith is not a disease with symptoms, but a gift that needs to be used wisely.
There is not a classic war of critical thinking and faith as many would believe. Many of the greatest minds in human history were religious minds, some even among the clergy of various religions. Powerful moments in human history were marked with both faith and religion working together. Our society cannot ascend as Sabby put it without acknowledging an integral part of being human, which is that we believe in things that are not readily apparent or supported. How can we rise if we cut away most of the people in the society.
Also, how do you intend to reform the Church when you do not care about the opinion or feelings of anyone that is religious or faithful? To state that you understand but don’t care is an extremely heartless statement. To say that people’s feelings are meaningless is an ignorant statement of someone that does not care to learn or understand another person. Faith and religion are personal parts of a person and their discussion should take that into consideration. That part of someone is an opportunity for dialogue, not heartless posturing. To further say that fact won’t sway your opinion only lends toward that image of the ignorant and dogmatic. Much as people accuse the faithful of being.
This is the problem with terms like 'faith'; it's a hugely loaded word. Yes, people work off 'faith', but not in the same way as a religious person, in most cases.
For example, if I'm dating a girl and we've been together five years. I believe she's not cheating on me. Is this faith in the same sense of religion? No. I've been with my this girl for five years, she's still with me and I have no reason to believe she's cheated on me. Therefore, it makes sense to assume that (at this moment in time), she isn't cheating on me. However, if this same girl has cheated on me several times? Yes, you're operating more on the logic of religious faith; you've got proof that your girlfriend is prone to not remaining faithful, so to wholeheartedly believe that 'She won't do it again' is hopeful thinking. People normally put their 'faith' into things due to past experiences, reasonable outcomes from reasonable expectations. And yes, faith does push people onwards; when you consider what a lot of faiths preach, are you sure that's what you want? Westboro Baptist Church is pushed forward by their hatred of sinners and homosexuals preached by their faith. The Pope preaches immorality and horrid atroscities because he believes an invisible man speaks through him. Religion, however, has not done good; people have done good. A man who is a Christian who helps another man out doesn't prove that Christianity is a good, moral system. It proves that this -man- is a good, moral person. Just like Stalin doesn't prove that Atheism is a cult of personality creating machine.
Also, a lot of large examples of religious good are actually huge evils; look at Mother Teresa, who is revered as a great woman of care and medicine, who actually put people through more suffering, stole their money and greated a cult of suffering and convincing people to embrace their suffering, rather than helping them to develop. My own religious beliefs has similar; the Dalai Llama, a huge advocate of peace, harmony and good will? Given money by the CIA to form militia training camps and, when in power, lived as a king amongst a people who were forced into peasantry to sustain this. Punishments from this regime included eye gouging, burnings, etc.
Lots of great minds were religious, sure. But, to me, this is a product of the times; religion is a huge filter on a person's world view, just like sex and colour was. If you weren't a Christian, good luck being accepted or being paid any mind. There's an entire movement (The Clergy Project) devoted to helping those within the faith who've lost their belief get jobs and fit back in with non-religious communities, as they're stuck within their religion for fear of not being able to support themselves or find social circles outside of it. However, just because we can explain one portion of something, it doesn't mean we can explain another, where religion finds itself; the Greeks knew the world was round. That didn't stop them believing a chariot pulled the sun across the sky, because they had no clue on how the sun circled the Earth.
One major part of reformation, for me, would be completely abolishing any idea that religion is anything different than any other organization. I believe they should be taxed. They should also be made to answer for the problems they cause, and promptly called out for it - if any other person went to countries and preaching death sentences to Africans (Don't use condoms, they don't stop HIV!), would they get away with it? If people had proof of mass child sex offenses and cover-ups within a business (The Vatican), would they be allowed to just keep doing it?
As Sabs said, your feelings in situations have no value. It has nothing to do with your feelings. It may upset some pastors that, say, they have to pay taxes, but paying faxes and bills also makes me sad. Does that mean I get a break from it, if I don't feel like paying and talk to an imaginary friend?