Ask any atheist. The reason we object to religion is because of the harm organized religions inflict upon societies. But the source of our disdain goes deeper than that, and believers are often left bewildered because we do not adequately explain the actual source, and, while religions indeed harm societies, they also help individuals grieve, provide hope, etc., etc. Without an adequate explanation, believers have little to doubt because harm is—in their eyes—a necessary product of a just god. So let me put it in eighteenth century terms to finally explain the source of our contempt.
David Hume’s 1739 A Treatise on Human Nature sums it up:
In every system of morality, which I have hitherto met with, I have always remarked, that the author proceeds for some time in the ordinary ways of reasoning, and establishes the being of a God, or makes observations concerning human affairs; when all of a sudden I am surprised to find, that instead of the usual copulations of propositions, is, and is not, I meet with no proposition that is not connected with an ought, or an ought not. This change is imperceptible; but is however, of the last consequence. For as this ought, or ought not, expresses some new relation or affirmation, ’tis necessary that it should be observed and explained; and at the same time that a reason should be given, for what seems altogether inconceivable, how this new relation can be a deduction from others, which are entirely different from it. But as authors do not commonly use this precaution, I shall presume to recommend it to the readers; and am persuaded, that this small attention would subvert all the vulgar systems of morality, and let us see, that the distinction of vice and virtue is not founded merely on the relations of objects, nor is perceived by reason.
[[Readers with access to APA PsycNET can access it here. Otherwise use google or visit your local library. See p. 469.]]
In other words, people tend to make pronouncements about what ought to be based on their beliefs about what is. This is a serious problem because what we believe ought to be does not necessarily follow from what we believe to be. This problem is exacerbated when we make pronouncements about what is when knowledge about the state of the world is impossible.
In the religious context, as far as I’m aware there are no religions that claim to be the truth with 100% certainty (although many religious people do). This is why religions teach to take things on matters of faith, which is a religious belief consisting of complete devotion despite a lack of evidence. In other words—let’s take Christianity—the followers of Christ follow blindly, yet they base their oughts on imperceptible pronouncements about what is.
Paraphrasing Matt Dillahunty: Demonstrate that your god exists before we can even begin to discuss the merits of your religion.
When Christians, Muslims, Hindus, or anyone else make claims about the way society ought to be without being able to first demonstrate that their god exists and their religion accurately reflects what their god wants, they are pronouncing policies that a) have no basis in objectivity, and b) produce in the mind and flesh of the outsider objective harm.
Hume hits the nail on the head. Before religious people can tell us what ought to be, they must first demonstrate what is: Does god exist? And what does god want? If you cannot answer both of these questions, then what you claim ought to be does not follow from your beliefs. Furthermore, by definition of faith no one claims to even know what god wants.
And as is patently obvious, science is fairly good at telling us what is. Methodological naturalism is the best tool we have for explanation. If we based our social policies on natural—read, secular—explanations then we’d make a lot more progress as a human species, and we’d avoid all the harm religions bring to society. No religion has a monopoly on explaining the is, only science can do that. As for the good that religions bring to society, this can also be achieved through secular means, and we wouldn’t even need to squabble over what a non-defined god wants.