The problem is not that Protestantism is worse than Catholicism, or that Islam is worse than Christianity, or that Christianity is worse than Judaism, or any permutation of those comparisons.
The problem is the basic premise that defines all of the monotheistic, patriarchal religions that keep popping up in the Mideast -- the "religions of Abraham." Their model of the human spirit is one-dimensional. Everything falls on a linear scale between "good" at one end and "evil" at the other.
Life and human beings are more complicated than that. You cannot reduce everything that people do and everything that happens to a one-dimensional measurement and judge it by saying, "that was very good," or "that was a bit evil," or "that person is a saint," or "that person does the work of Satan."
The polytheistic faiths, which the Abrahamists have done their best to stamp out, had a much better model. We all have multiple "spirits" inside us that vie for control of our consciousness and for dominance of our personality. Each of them can be a force for good in the right circumstances, and a force for evil if allowed to guide us at the inappropriate time.
There is a Warrior inside each of us. If someone is attacking your family with a machete, it is really handy if the Warrior can seize control of you and give you the focus and courage to overpower the attacker or even kill him if that is the only way to save your family. But it is a disaster if the Warrior takes control and seduces you into going over and overthrowing the government of a sovereign state and destroying its infrastructure, just because the people who live there happen to speak the same language and practice a similar religion to the people from a different country who crashed airliners into your skyscrapers.
There is a Reveler inside each of us. At the end of a long hard week of work, it is healthy for the Reveler to help put that week behind us and have some fun, without ruining ourselves with worry that we'll just have to go back and continue the work on Monday. But it is unhealthy if the Reveler is still in control on Monday morning and guides our hand to turn off the alarm clock and go back to sleep.
The same can be said for the Hunter, the King, the Lover, the Healer, and all the other archetypes inside us (in Jung's language) or all the other gods who influence us (to use the language of an older but equally valid model).
The Judeo-Christian-Islamic model of our spirit is so oversimplified that it is useless at guiding us through life. Life's choices rarely are a matter of good versus evil, but simply of figuring out a complicated situation and looking for a resolution with maximum benefits and minimum drawbacks. Offshore outsourcing, giving two Indians the job of one American: Good or evil? Driving an SUV because it's easier to buckle your child into a car seat, even though the vehicle itself is more likely to cause an accident and harm another driver: Good or evil?
But philosophy aside, it's also possible to judge a movement by its results. What have the Abrahamic religions contributed to humanity? Every time one of them reaches its zenith, it seems to coincide with a period of abject humiliation for its practitioners. The period when Catholicism was the universal religion of virtually all of Europe is the same era of unbelievable ignorance and sqaulor known as the Dark Ages. For Protestantism it was the half millennium that saw the extermination of the native civilizations of the New World and the repopulation of the hemisphere with slaves brought from Africa -- an era that also added the terms "World War" and "Holocaust" to our lexicon. The golden age of Islam was a time when "infidels" could be summarily slaughtered merely for being "infidels." If the modern state of Israel represents the culmination of several millennia of Judaism, its inability to make peace with the Muslims in its midst -- no matter how admittedly difficult a task that may be -- does not distinguish it as an honorable faith.
Jung summed it up well and concisely: "The wars among the Christian nations have been the bloodiest in human history." If the war that many predict between Christianity and Islam comes to pass, we will surely see that statement trumped, with both sides fighting to impose their version of a montheistic, patriarchal culture on the whole world.
I have never understood what motivated so many people to join the various movements preaching the existence of only one god -- who just happens to be male. But the results of the ascendence of that model have proven their efforts to have not only been wasted, but, in their own terms, to have been works of "evil."