I was asked in conversation not long ago what bothers me most about religious thinking. First, I have to say that I am not truly bothered by religious thinking. I believe it to be a part of the human experience in many ways. While it is not a part of my own experience as I live my life, it does not bother me that others have it in theirs. But I am bothered by some versions or aspects of it.
First and foremost, I am bothered by the use of religion as science. Religion should not be used, in my opinion, to make factual statements about the world or universe. Religion involves the acceptance of certain things as fact without regard for evidence. This is what is called faith. We all have faith in things, whether religious or not. We wouldn't get very far without faith. However, it is important to recognize that faith in something is not sufficient to regard that thing as some kind of universal truth.
For that reason, I am bothered by, for example, faith healers, who believe that praying for someone's recovery from a physical ailment will bring it about without the intercession of medicine. There is no evidence for this, but there is evidence for medicine. Foregoing medicine for faith healing is erroneous and wrong-headed. I have no problem with someone praying in addition to medicine, but you cannot replace medicine with faith.
Another thing that truly bothers me is when people use religious reasoning in public policy debates. Saying that homosexuality is a sin in God's eyes is not sufficient reason for denying gays the right to marry. You have to be able to demonstrate what harm would be caused to others by allowing gays to marry.
I recently read an article in the New York Times that gave a good, detailed explanation of the reasoning of evangelicals in regards to the governance of the United States, and it just killed me. The idea that there are enough people in the country willing to vote for someone because he or she will help usher in the glorious end of the world is a little funny but very scary. It is the same sort of thinking that grips those in the Arab world who believe they will attain glory by blowing people (including themselves) up.
The very worst aspect of religious thinking, though, is that it can be co-opted by anyone with sufficient charisma and steered towards destructive ends. The fact that it requires no evidence, only faith, means that nothing more is needed than the words of a person who claims to know the Truth. The most egregious example of this sort of thing would have to be the Catholic Church. Millions of people across the world believe that a single man is the primary conduit for God's word. He lives in splendor and riches provided to him by the (often very poor) faithful, preaching about a need to help the poor and about the virtue of poverty. The friction between the stated belief of Christianity and the gaudy glamour of Catholic churches and cathedrals and such doesn't stop this from happening. For many Catholics, the thought process is something like, "Sure, these things seem to be at odds, but the Pope is the word of God on Earth, so the flaw must be in my understanding." This is the "mysterious ways" defense of religion that can be used to gloss over any set of inconsistencies.
Obviously there are plenty of other examples of this. Cults of personality are not confined to religious institutions either. Hitler's rise had little to do with religion, for instance, though the Nazis had the same sort of religious thinking - belief in a concept regardless of evidence.
People can be made to feel that just about anything is true. That is the very reason that science exists. It is a confession that we are flawed in this way and need some external means for estimating the truth of things. I say "estimating" because a core aspect of science is that even its most seemingly sacred tenets can be challenged using the same methods that brought them to their exaulted status. Recently, scientists observed a particle traveling at speeds that seemed to refute one of Einstein's core theories upon which much of the physics of the past hundred years has been based. That sort of thing just doesn't happen in religious circles. Science admits that we can never be completely certain about anything, but we can develop better estimations of the truth by manipulating the world around us and seeing what happens.
And this is something that rings very true to me. I don't believe it regardless of evidence. I believe it because of evidence. Thousands of years of praying to God for a cure never had nearly the effect of the development penicillin.
Maybe there is a God up there somewhere. Maybe he's playing with us like dolls, or we're in some kind of video game like The Sims, in which we are just pawns at the mercy of some occasionally sadistic player. He certainly can't be the omniscient, omnipotent, ominbenevolent, omnipresent being I grew up being told about, as such a being would not have created this cruel and unfair universe (though I'm sure I'd be told that I see it as an inconsistency only because the human mind lacks the ability to see God's glorious grand plan for the wonderful thing that it is). I don't see any good reason to lob prayers at him, but others can go do that if they want. It doesn't seem to hurt.
I guess you could call me an apatheist - I don't really care if there is a God or not. It's not an interesting question to me because it's completely unknowable, untestable, and without impact upon anything in my life. If he wants me to shower him with praise, well, he's never told me so. As far as I can see, those orders came from people, and they didn't have much backing them up. If he wants me to behave a certain way, he hasn't told me or given me any good motivators to do so. There are various groups of people all over the world who are absolutely certain that they know what God wants, spouting off a variety of wildly inconsistent truths.
So I just live my life as if there is no God, and I think I'm happier for that.