Firstly, a question: "Has anyone heard of the Euthyphro dilemma?" In one dialog of Plato 2400 years ago, our interlocutor demonstrated the absurdity of morality coming from a divine source. "Is the pious loved by the gods because it is pious, or is it pious because it is loved by the gods?" Similarly: "Is the good loved by the god(s) because it is good, or is it good because it is loved by the god(s)?" All of the attempts to try to get past this dilemma are based on attempts to make the definition of god malleable enough to make good and god one in the same. This does nothing because by defining god as good, the term good then loses its meaning; an action is called good only because it is what god did; if he had done something else, that would have been good as well. Of course, should I do the same, somehow I may be charged with a crime. Hence, the action must have a level of goodness to it even if not done by any gods. Aquinas' sophistry is no rescue.
Further, within the moral context of religion, we are truly doomed. Take religious belief X and religious belief Y. According to the X religious moralist, the things deemed good and evil by the deity of X are in fact good and evil; similarly is the case for the Y religious moralist. We know from experience that certain religions will have different moral precepts, otherwise what distinguishes them are inconsequential. Judaism does not allow the eating of pork; Jainism does not allow harm to come to even the smallest creature; the Mezo-American religions of the past had human sacrifice; homosexuality is taboo in many belief systems; etc. Within this context then, how does a moral sanction in X and another in Y work with each other? What I mean is this: in X, some moral precept will be different from that in Y; in fact, X may call something in Y immoral. He says this because of X. Y does not accept this because of the precepts of Y, and Y may even charge X with similar statements of immorality. An example of this can be the case of homosexuality. Some churches today say it is sin; others are not claiming it is sin or wrong at all, even though they read the same holy book. Further, by condemning homosexuality, the latter church could claim the former church was acting immorally because of how they treated homosexuals and make them feel guilty unnecessarily. Both churches can make opposite claims, both claim that they are being moral, and claim the other is being immoral.
A certain word should come to mind here: relativism. That is what we have here with this situation of different religions. And it is ironic because the theist claims morality from god to ensure that it is absolute and not relative. And it is not always just about minor issues of what you can eat or how long your hair should be. We also have to deal with the oppression of half of the population because of their estrogen levels; countless holy wars have been issued based on revelation and textual clairvoyance; the nether-reaches of people are hacked away at; who you can commune with is limited; the examples are without end. And you would be hard-pressed to find agreement on these issues even within the larger spheres of any many religion. The Christians cannot agree about apostolic tradition or homosexuality or contraception, for example. And the things that almost all people would call evil has happened in the name of these theologies.
Now, one often hears the retort that we just need to weed out the bad theologies and leave the good ones. And how are we supposed to know what theologies are good and bad if what is good and bad is based on theology? The statement supposes that that person has the superior belief simply by the fiats of that belief. And the same statement could be made by Pope Urban II who preached for the First Crusade. From a religious morality, one cannot claim another religion is better than another without invoking some sort of absolutism, but that runs contrary to the very nature of religious morality--it is relativistic. This or that is good based on this or that theology.
Within the religious paradigm, one cannot claim that another religion is bad or immoral without becoming ridiculous. X and Y are in conflict, so how does another person, P, decide which is the one with the better morality? How can P say that Y is being immoral or X is? There are three choice: decide X is true; decide Y is true; decide that there is something other that X or Y to judge by them. Taking the first two options is without merit because it is a decision not based on morality because you are choosing that morality. The choice hence relative and meaningless to the person that chooses in an opposite case. To claim anything in X or Y is good or bad requires something to supersede both, and hence a morality must exist that is not based on any of these theologies. One may try and suppose a higher theology, but that only leads to an infinite regression.
And so we have secular ethics, being it utilitarianism of Kant's categorical imperative or something else, including our ethical instincts. It is the only thing that can possibly supersede the religious bickering and say that some theology did cause evils. The religious person cannot do that without contradicting themselves. If they claim that religions is the source of morality, but say some religions is immoral, then religions is a source for immorality; any religion can make the same statements, so they all contradict each other, all fall into relativism, and often violence ensues. Religious ethics causes only absolute relativism, the most dangerous ethical precept of all.
Can't all of these pundits on the radio or TV not see the contradiction in their statements, in saying religions does cause evils, but claim religions are causing evils within the religious context? All they can say is that the believe something is immoral from their perception of their theologian, which cannot cross over into another religion, perhaps not even another sect. In the case of sects based on the same holy book, one could claim that someone has a theology that is not based on that book, and so their morals coming from that sect are not true; however, it seems that such arguments of who has the correct interpretation are not going to be settled in any point in the future. The Pope has confirmed all non-Catholics are not "real" Christians; Shia and Sunni Muslims certainly do not agree about Ali and the imams; there are plenty of permutations of Judaism; Buddhism can be atheistic; sectarianism is without end. The relativism of interpretation is much the same as that relativism of morals--and worse is that it is absolute.
One cannot escape this problem. If one claims that someone is evil in the name of religion, they first have to demonstrate how it is good; but that religion was not chosen based on its goodness but on the sense of what that person already thought was good, meaning that that sense of morality must have existed before he chose; otherwise, the choice was ad hoc and carries no real weight. If morality is not relative, it must exist beyond the religious fray. Otherwise, we cannot say one religion is good and another is not.
As for most people, they should realize this, since they are not taking all that they have in their holy books to heart. Most people pick and choose what is right and wrong in their books. That choice cannot be made within the confines of that religion. If the book says "murder all infidels", you cannot within that same religious sphere of morality say that that is not a moral statement, even if it contradicts another passage, such as "don't kill, EVER". And how are those choices even made? Intrinsic understandings of what is good without the book. And fortunately, most people do not take every word of their holy books are strong as the next. Otherwise, we would be in the days of the Inquisition all over again. If you say the Inquisition was an immoral institution, that statement cannot be within religion.
Face it: you are moral because of some other factor--you know that acting morally is favorable in most cases. Why else would morality be called "good"? So, I ask that we realize that the basis of morals on religious leaders. Even Jesus was supposed to have said "Why do you call be good?" (Mark 10:18).