Some religions are more harmful than others
Given that some or all religion is harmful to society and believers, some atheists argue that certain religions or denominations are more harmful than others. Believers generally think their beliefs are superior to other religions. However, comparison of different religions among non-believers is controversial.
The opposing view is that all religions are equivalent and are equally harmful. The idea is sometimes based on the concepts of religious toleration, religious pluralism or postmodernism. However, the belief that religions can peacefully coexist is possibly true for only some religions.
The question of how much evidence supports a religious belief, or how true it is, is a separate issue.
Sam Harris argues that not all religions are equally harmful. He is particularly critical of Islam and commented that "We have to be able to criticize bad ideas, and Islam is the Mother lode of bad ideas." In explaining this statement, he said:
"I think that we have an idea here that all of the religious are the same, that they are all equality wise, or equally empty or equally irrelevant. And obviously devout believers of various religions don't believe this but secular liberals believe this and it's just not true. Our religions are quite different and there are many cases in which Christianity is worse than Islam, if you are going to talk about something like opposition to embryonic stem cell research. [...] We have to acknowledge that Islam has doctrines like jihād and martyrdom and death to apostates which are central to the faith in which they aren't in other faiths. [...] These beliefs, though held for identical reasons (faith) and in varying degrees by individual practitioners of these religions, could not be more different. And this difference has consequences in the real world."
Jainism is sometimes cited as an example of a non-violent and therefore less harmful religion than the Abrahamic religions. "The crazier you get as a Jain, the less we have to worry about you."  Arguably, extreme non-violence might be harmful to society in some situations.
Inaccurate characterisation of religion
Arguably, a religion is not defined by its holy text but rather by the beliefs and behaviour of the mainstream view of the religion. Since many Muslims either do not take the Qur'an literally or are unwilling to act upon it, the Qur'an is largely irrelevant in attempting to characterize what Islam stands for.
- "It's not like people who are Muslim who do wacky things have a monopoly on it. We have hypocrites across faiths. Jewish, Christian who say they are for God and end up doing [terrible things...] Here is my difficulty with your premise: look at religions over history have had things done in their name that have been terrible. [...] You are making an error in that Islam has over 1.4 billion adherence. There is a heterogeneity to it [i.e. a diversity of beliefs]. Are there extremists who are horrible people, who would slit your throat? Yes. But there are also folks that are fine upstanding people."
This defence does not apply if extremist or intolerant views are held by mainstream believers, such as death for apostasy, which is a relatively mainstream view of Muslims. According to a Pew Research Center, this is the majority view of Muslims in Malaysia, Jordan, Palestinian territories, Egypt, Pakistan, Afghanistan.  It is a significant minority Muslim view in many other countries, including in industrialised democracies. Adjusting for population differences, the overall average support is 36% and the poll covers countries occupied by 52% of Muslims.  While the view has only minority support in many countries, this suggests that there are many other Muslims that would support persecution of apostates but do not go as far as calling for their death.
It is difficult to evaluate the effect of religion on societies because their effects are widespread but subtle. There is no way of having a control group and imperfect comparisons must be used. Many negative social effects may be caused on other non-religious beliefs that happened to exist in a particular culture. The spread of a particular religion may also be accompanies by the spread of non-religious ideas. It is difficult to distinguish between to two.
- "Unfortunately, some parts of the religion have bled into the culture. And some parts of pre-existing culture have bled into religion. "
The different levels of support for Sharia law and the death penalty for apostasy for various countries suggests that there are cultural factors involved. Simply being Muslim is not reliably predict a person's views.
Also, it is difficult to characterise exactly what is meant by "religion", "Islam" or "Christianity". Arguably, this criticism is an example of Loki's wager.
While not directly refuting the general argument that some religions are more harmful, religious critics face counter-arguments that their view that a specific region is more harmful is biased, cherry picking or based on double standards. For instance, countries that are supposedly "Christian" launch many wars of aggression (sometimes with a pre-text of liberation) both in modern times and throughout history, such as the Crusades. Therefore, it seems unfair to claim that Islam is more war-like than Christianity. 
Claims of bigotry
Criticising a specific religion is sometimes considered a bigoted opinion. Critics of Islam are sometimes accused of Islamophobia. This argument changes the topic of discussion away from Islam and on to the negative qualities of the critic and is therefore an ad hominem argument. Criticising beliefs of people does not necessarily imply that the believers are automatically hated by the critic.
A similar ad hominem argument is to disparage the understanding of a critic without directly addressing their argument:
- "Now hold on—are you the person who understands the officially codified doctrine of Islam? You’re the interpreter of that? "
This is the unreasonable claim that only experts may have opinions.
Rejecting the comparison
Some non-believers argue that it is pointless or counter productive to attempt to compare religions in this way.
- Friedrich Nietzsche, Twilight of the Idols, 1889
- CNN, Harris: Islam is "mother lode" of bad ideas, 13 Oct 2014
- Sam Harris, Lecture at the First Congregational Church of Berkeley, November 10, 2010)
- Poll analysis
- The Young Turks, Ben Affleck Angrily Defends Islam Against Bill Maher/Sam Harris, 6 Oct 2014