A lot of ink has been spilled explaining how religion goes wrong, becomes evil or turns violent. Here's a whole bunch of religion-slamming memes, just for fun. Lately, pollsters and religious commentators have been tracking the "rise of the nones" (those with no religious affiliation in America, now as many as 20%) and religious leaders are writing a lot about why various demographics (mostly White 18-40 year olds) have left church behind, who is to blame (ie. what is wrong with the way people are "doing" religion) and what they can do to win them back.
The thing is, in my opinion, religion (and here I mean religious communities or people, because "religion" and "religions" don't really exist except as words or theoretical constructs) goes right and wrong along basically the same lines, and frequently people react to it from a personal perspective that corresponds to these basic lines.
First of all, "religion" is essentially communal, as are human beings. I'm not going to try to prove this. I like William James' Varieties of Religious Experience just fine, but everything we call "a religion" has a strong communal element and would not exist very long without it. Likewise for human beings.
Second, every functional community (religious or otherwise) has rules to inform and guide moral behavior, prevent its members from injuring each other and establish boundaries (what does it mean to be part of the community; and "insider" or an "outsider"?).
Third, most of the rules of most communities make some rational sense. I remember reading a book by Marvin Harris called Cows, Pigs, Wars and Witches: The Riddles of Culture, which explain how many cultural norms that seem strange to outsiders actually contribute to the survival and functionality of the communities that hold them. For an example of my own, is a prohibition on non-marital sex and a prescription for lifelong marital fidelity really a mysterious and irrational rule for a community? Every community that has experimented with "free love" in the past 200 years has been a failure. Human beings seem to have some innately possessive ideas about sex that cause huge relational strain when they are violated. If some community wants to try to reinvent the wheel on this, I guess they can try, but I'll be surprised if they are still a community in 20 years.
Fourth, human beings seem unavoidably drawn to the idea of transcendence, something beyond and bigger than themselves. It might just be "the community," whose values then also take on transcendent status ("freedom" "rationality" or what-have-you) but more often transcendence seems to have a divine-personal face, like God, gods or ancestral deities who also sanction (or provide) the community rules.
I think the short list of genuine complaints against religious communities comes down to lack of adaptation to context, and the use/abuse of violence and coercion. Of course these complaints and criticisms assume a set of foundational values that are also somewhat communal and absolute (transcendent in their own way). It's also reasonable to ask why (given their transcendent status) religious communities should adapt their rules or disavow the use of violence and coercion in support of such rules unless adapting rules and disavowing force is in fact part of the rules (Stephen L. Carter's article "The Free Exercise Thereof" in William & Mary Law review, Vol. 8, No. 5 is excellent on this point). It's also reasonable to point out that most existing religious communities have already adapted their rules to some greater or less extent. Sometimes "too little, too late;" other times "better late than never."
So religious communities basically go right and wrong at about the same point. They go right when they try to act like actual communities, which nurture and cultivate the human beings of the community into ways of behaving that honor the basic communal existence and individual honor of human beings. They go wrong when life gets more complicated. For instance, when it must relate as a community (charged with the care of its own) to other communities with competing interests, or when the genuine interest in the cultivation of a specific individual (or set of individuals) within the community competes with the genuine interest of another specific individual (or set of individuals). This is basically the argument of Niebuhr's Moral Man, Immoral Society (see Gushee's post here). Violence is not the only possible outcome. The "rules" are supposed to help work these things out, but sometimes new situations arise, and in a large pluralistic society (like the U.S.), sometimes it's a lot easier for an individual in question to jump ship (or be thrown overboard), than to really work it out.
In America, individualism combined with the "failure to adapt" criticism is probably 90+% responsible for the "nones." In other words, it's not that the religion has gone wrong, but the particular community-oriented rules of a religious community rub individuals (who have not been conditioned to community-oriented life) the wrong way. A national-community, with values of privacy and self-actualization and a gigantic legal code (ie. "rules") to support these individualistic values, is doing a better or more comprehensive job of forming the minds and assumptions of a large segment of the population than any traditionally religious community.
Then again, David Dark and David Foster Wallace would both say that there are no actual "nones."