The major problem with religion is that it profoundly enforces an agenda that is harmful specifically to those that are not considered "normal" by society at both the given time that the religion is formed and at the present moment should that religion still be practiced.
We hear of three major things being told of in religious texts:
1) Divine beings,
2) How we came about, and,
Number one simply proposes that there is a master at work, controlling and forming our world as well as ourselves. This proposition was accepted because for the longest time in the history of human civilization, we had always had some sort of monarch or alpha-male watching over us. It was what we were used to, and therefore it made sense.
Number two is simply an explanation for the creation of the universe. Going hand-in-hand with the ruling monarchy point I made earlier, since kings built cities and nations, (yes, technically their underlings did, but these people pretty much never received credit when it was due) the idea of something having always been (other than a god) had been a foreign idea and therefore creationism was an essential philosophical viewpoint at the time.
Number three is a set of rules imposed on the religion's followers that are used to distinguish "right" from "wrong" in society. Many times, morality is seen as intrinsically good, because we only view morality as a principle of good things to do instead of a distinguishing system of both good and bad. Morality establishes social norms which, in conjunction with the ruling elite point I made earlier, work to the advantage of religious demagogues and established (or very nearly established) governments and align with the viewpoints of said demagogues/officials.
The essential conclusion to then be made (in my opinion) is that religion has in the past simply been a system scripted to keep people in check. We see this most obviously in the Hindi caste system, where people are supposedly born into poverty or riches due to the actions of a past life. We see this slightly less so in extremist Islamic culture where non-Muslims are seen as Infidels and those that don't conform to the poorly-aligned and obviously biased viewpoint of religious authors are doomed to be persecuted if not simply murdered. And less obviously we see it in the Christian religion, where a social norm of Christian heterosexual male (CHM for short, I guess) dominance is presented via not only implied glorification of the CHM, but also explicity calls for persecution and inferior treatment of "lesser" individuals.
So why, then, is this being enforced?
Obviously, religions have gone through several changes that have made them more tolerance oriented and love-slanted. But until we destroy this facade of "morality" in these systems, we end up doomed to drift to and from different morally-acceptable societal norms, and these norms will most definitely be exploited by those willing to do so for their own personal pleasure.
One could even go so far as to say that the theist-oriented concept of creation was specifically included in this code of morality in order to conform people to the idea of a monarchistic ruler as well as an all-knowing, superior enforcing body of this moral code.
Think about it, if someone's standing over you with a gun pointed to your head telling you to follow a set of rules, you're obviously exponentially more likely to follow them. What if the gun doesn't have bullets? Doesn't matter, there could be a bullet in that chamber and most people are (reasonably so) not willing to take that chance.
Then you get into the idea of spreading religion, where religious figures request that you spread your message so that you save other people from this person with a firearm trained at the head of every individual. And so when someone tries to stand up and challenge the person on whether or not they're a real threat, everyone screams for them to sit down. Sometimes, people are even taught that allowing someone to be killed will mean their death as well. In which case you then have people violently and oppressively forcing skeptics to sit down.
Are you seeing what I'm getting at here? This system of a god, of a religion, of a moral code, it has always been in some way shape or form, even if in very small amounts, inhabited by a group of people who want to bend a philosophy of how we were made into a system of control that tells us how to think and how to live. A system that develops a social hierarchy and then conforms us to it in the same package.
So even if a religion was created with the best of intentions, it will inevitably be manipulated into a method of gaining power over people.
Just my two-cents. Who knows, I might be a crazy idiot.