Many religious believers, and even some atheists, have occasionally claimed that religion itself is not inherently harmful. Instead, they contend that the problems caused by religion are actually the result of organized and institutional religious bodies. And while a significant portion of these issues may be due to the organized aspects of religion, organized religion is not the only source of harm. It is part of the problem, and it is a problem, but it is not the problem exclusively. While not all religious belief is necessarily harmful, the damage that does arise from religious belief would not be wholly eliminated with the end of organized religion.
It is, of course, unavoidable that religious organizations have many problems that are specific to their nature as institutions. If they have a leadership hierarchy, it's possible for that leadership to become corrupted in various ways. For instance, a religious institution could potentially have a problem with rampant child abuse, and be directed by its leaders to avoid reporting this to law enforcement. Organized religions can also establish their own doctrines and dogma which their clergy and members are required to abide by. Depending on the content of their beliefs, this can be used for good or bad purposes, but it is nevertheless a blunt instrument. Simply being among a great number of people who appear to share your beliefs can discourage critical examination and doubt.
A religious body can be capable of exerting social pressure on individuals in a very focused way. A person's social network, possibly including their own family, may be based largely in a certain religious community. This organization then has the power to influence that person and discourage any dissent by instructing their fellow adherents to shun and exclude them until they do what's demanded of them. This can also be accomplished less explicitly by promoting the idea that a certain religious group is the only way to salvation, and the rest are terribly mistaken. This doesn't leave much room for disagreement.
Religious organizations are especially well-positioned to mobilize their followers for political purposes, as demonstrated by the efforts of the Catholic Church to encourage parishioners to fight against gay marriage in California, Maine, Minnesota and Washington. While this could potentially be directed to more positive goals, it still presents one group's religious beliefs as a basis for public policies that affect everyone.
All things considered, it isn't looking very good for organized religion. But religion, whether it's organized or not, comes with a variety of problems that its organizational aspects are not solely responsible for. For example, polls show that people who attend church more frequently are less likely to support gay marriage, and vice versa. This pattern has also emerged in polls of Catholics specifically, whose official religious doctrine opposes gay marriage. But what is the nature of the relationship between church attendance and personal religious fervor? Do people become more religious as a result of attending church? Or do they attend church because of the strength of their belief? Could both of these attributes be linked to an unidentified third factor? None of this is ruled out by the data, and neither is any of it singled out.
While it makes sense that exposure to organized religion in its various forms would have an influence on one's religious views - especially among youth who didn't get to choose whether to participate - it makes just as much sense that religiously inclined people would tend to gravitate toward religious bodies. Although it can be appealing to imagine that religious organizations originated as a conspiracy of social control - an impression that the actions of many religions have done nothing to dispel - it seems more likely that religious groups developed organically. Religious people, like anyone else with a certain interest, will try to seek out like-minded individuals. They find others who share their views, and they embark on a common enterprise.
It might be nice to think that ending religious organizations would suffice to end religion entirely, but many people have religious impulses that would persist in the absence of their favored religious group. Even if it were possible to "disorganize" organized religion and scatter it to the ends of the earth, religious people would once again discover that there are others like them, and they would regroup.
Without religious institutions to channel and coordinate believers, many of them would still be disposed to certain patterns of thought and behavior which can be hazardous. You don't need to attend religious services to think that spirits are conversing with you and giving you their personal attention. You don't need the affirmation of a religion to believe that deities are handing you the only correct answers and anyone else who says the same must be wrong. You don't need hymns and homilies to attribute natural occurrences to divine intervention. You don't need a pope or an imam to think it's okay for you to believe something for no reason beyond simply wanting it to be true or feeling that it's true. You don't need official dogma to act like your ideas about God are a sufficient basis for depriving your fellow citizens of their equal rights - or killing them for insulting someone you call a prophet.
All this requires is an incomplete understanding of secularism, liberty, ethics, reason, and the natural world. Organized religion may facilitate such manifestations of ignorance, but make no mistake: they can and do flourish without it. People are born this ignorant. Religious belief provides a focal point for that, and organized religion offers an especially elaborate template for people to subscribe to wholesale. But this ignorance is the default state of the untrained human mind, and it's a breeding ground for superstition.
Organized religions are often subjected to criticism simply because they're such a convenient target. They're so visible, powerful and active that it's very easy to point out when they do something wrong - especially when they do a lot of things wrong all the time. When individuals are singled out, it's typically because they're a representative of a given religious group, whereas it would seem unnecessary and petty to point out that John Q. Unaffiliated God-Believer is being epistemically irresponsible. But he is, and on a large enough scale, this snowballs into a significant issue. There's a tendency to miss the trees for the forest and treat religion as a separate entity from the individuals it's composed of. In truth, the problem of organized religion wouldn't and couldn't exist if it weren't for religious people.