For the most part I'm happy to leave people to their beliefs. I know that life as a human is often brain-gratingly hard, and there's a lot to be said for finding things that make it all seem worthwhile. I know, too, that rationality isn't everything; that at a basic level, expecting humans to be thoroughly rational implies a misunderstanding of how we work and what motivates us. Largely as a consequence, I suspect that many questions will always resist resolution by rational, scientific means. People need meaning in their lives, and science struggles with that.
So I can understand the appeal of religion, and I find it hard to begrudge anything that helps someone get through life without making things harder for the rest of us, but all the same, a lot of religious beliefs upset me. It's not so much that I think people are being stupid - that's largely beside the point. It's more that their beliefs imply ideas about justice and morality which are downright abhorrent.
The most fundamental problem, for me, comes of believing that there is a higher power in charge of the world (and concerned with human beings) that is both just and all-powerful. The fact is that this implies there is no improvement an omnipotent being ought to make in the universe, which implies that you believe that all is right with the world; that human life is just as just as it ought to be.
So much of theology seems to be devoted to trying to weasel out of this, but I don't believe it's escapable unless you discard one or more of the supposed defining features of God. If God-the-Omnipotent wanted to change things in any way, They could. If God-the-Just thought there was anything wrong with the world, They would.
The Problem of Evil is fatal, but evil in the normal sense is quite a small part of the problem here. Free will does not require that people are motivated to act like arseholes. Give people some degree of autonomy and a limited ability to identify with others, raise them in a world where they're constantly struggling to get enough to eat, they suffer headaches and sore teeth, and where exerting power over other people helps them achieve their in-built needs and desires... and you're going to get them dominating and lashing out at each other. Give them plenty to eat, good health, useful things to be getting on with, and a strong sense of empathy, maybe you'll see different results. God, it seems, has chosen not to go that way - at least, not most of the time. Presumably this must be because steering very far from that path is in fact the right and just thing to do.
Likewise diseases, natural disaster, infirmity - the only coherent explanation for these within the framework of a world overseen by a benevolent, omnipotent deity is that they are somehow good things. Christians, Muslims, Hare Krishnas, Jews, if you believe in such a God, you are telling me that you think it is a good thing that I have a sore throat.
It is a good thing that the world is so constructed that the powerful gain by dominating the meek.
It is a good thing that many people have wheat allergies, often without knowing it.
It is a good thing that several million people die every year because for any number of reasons, the cells of their own body one day forget how to stop dividing.
I'll stop listing there, because we all know that life frequently inflicts grievous harm on us, often apparently at random. In addition to all these marvellous features of life as a human on this physical plane, many theists insist further that God's justice extends to eternal damnation; to punishments for acting on desires which are seemingly both harmless and innate; to condemning everyone who either couldn't accept religion at all, or simply failed to settle on The Right One. They even go to war in the apparently sincere belief that this is what their god would want. Even if both sides are doing that, no supernatural force ever sees fit to set them straight, presumably because sectarian conflict is just peachy with them.
You can probably see where I'm going with this. This stuff is quite plainly not just. It's not right. If there is an omnipotent and concerned God, this is what They want, or else things would be different. So God works in mysterious ways, and from a cosmic, divine perspective, perhaps all this stuff looks fine and dandy... but I'm a human, and the chances are you're a human too, and from a human perspective there is a great deal that is very wrong with this world, and only some of that is stuff that we can fix ourselves. The promise of a pleasant afterlife, especially one restricted to people who happen to follow the correct religious injunctions, does not negate that.
So if we suppose that there is an all-powerful God paying attention to humankind, then believing Them to be concerned with justice - or to care about us as humans - requires notions of justice or caring that to me are not just ineffable but, if you stop to think about them, profoundly offensive.
Having said all this, I should acknowledge that despite the most commonly seen descriptions of God fitting this pattern, many religious people do not take for granted all three of the characteristics of God that make these conclusions inevitable, and abandoning any one of them makes it possible to hold coherent beliefs that don't rest on a noxious conception of justice. It is not obvious to me why anyone would worship a God whose morality bears no resemblance to ours, or who is just not that interested in us - but then, I'm told that worship is for the benefit of the worshipper, so maybe it doesn't make that much difference what you worship.
The fact remains that we have people in public office who believe that there is a God in charge of this planet, who has given Their blessing to all those things that you or I might see as being horribly wrong with it. There are people in positions of responsibility who are completely fine with the idea that hundreds of millions of the people who are currently alive - almost certainly including me - will spend all eternity in Hell. Call me crazy, but that makes me more than a little uncomfortable.