In the course of this analysis, I will approach the claims as an empiricist with a scientific worldview so as not to prejudice my conclusions. For the convenience of the reader, I will perform my analysis in parts, taking two of the author's claims at a time.
3. Religion makes a virtue out of faith.
The author really doesn't provide any evidence for this claim beyond the anecdotal, but I will help because I'm a swell guy like that. The Catholic Church holds very specifically to the idea that faith (along with hope and charity) is a virtue of great importance, specifically faith in the Christian conception of God. This claim has (yet again) the same problem as previous claims made by the author; the evidence isn't strong enough to support her general conclusion. Let's take for example the Buddhist religion (a religion to which I seriously considered converting ten years ago). The below quote from the discourses of the Buddha in the Pali Canon illustrates the problem with the author's claim that religion in general teaches its adherents to trust authorities rather than trusting their own thinking.
"Do not go by oral tradition, by lineage of teaching, by hearsay, by a collection of texts, by logic, by inferential reasoning, by reasoned cogitation, by the acceptance of a view after pondering it, by the seeming competence of the speaker, or because you think, 'The ascetic is our teacher.' But when you know for yourselves, 'These things are unwholesome; these things are blameable; these things are censured by the wise; these things, if undertaken and practiced, lead to harm and suffering.' then you should decide to abandon them."
This portion of the Buddha's discourses is perhaps why some have claimed that Buddhism is an atheistic philosophy rather than a religion, but the evidence is strongly against that view, what with the Buddha's references to deities and demons along with heavenly and hellish dimensions in his discourses. So we know that not all religions train their adherents to trust authority rather than their own minds, but could the author retreat to the view that Christianity trains its adherents in such a way? Well, that would a difficult argument to make in light of the diversity of Christian views in the United States, which seems to be the only place the author has any limited experience with religion.
Most American Christians who belong to one of the hundreds of post-Reformation era forms of Christianity have a "subjective and individualistic version" of the doctrine of sola scriptura, which is the idea that the Bible alone is the rule of the Christian faith. And that statement was made by a Reformed Christian who believes the doctrine of sola scriptura, lest the reader think that it was a prejudiced remark. He is exactly right that most U.S. Christians have a subjective and individualistic understanding of the Bible, choosing to trust their own thinking rather than trusting an external authority to tell them what the passages of the Bible mean. Given this, the author should perhaps have more sympathy with religious folks who take those Iron Age views by virtue of trusting their own thinking.
But could the author fall back to the position that ancient Christian Churches such as the Catholic, Coptic, Eastern Orthodox, and Oriental Orthodox churches train their adherents to trust authority rather than their own thinking? Yes, at least on matters of pertinence to the Christian faith. On other matters like physics and biological evolution, the adherent is taught to respect the natural sciences as an authority. Even in the much-cited case of Galileo Galilei, Pope Urban was actually a patron to Galileo who provided him with funding for his scientific endeavors until he wrote a book that made the Pope look like the idiot in his dialogue. The Catholic Church has since come to accept the modern view of cosmology that is neither geocentric or heliocentric, and many Catholic clergy have been active in the natural sciences since there were natural sciences. So it would be difficult to even make the broad claim that the ancient Christian churches teach a general trust of authority rather than a trust in one's own thinking.
But could the author fall back to the position that at least with regard to theology and morality, the ancient Christian churches teach their adherents to trust the authority of the church rather than their own thinking? Yes. And this may or may not be a problem. The fallacy of the argument from authority is only a fallacy when we appeal to an authority without the necessary expertise to advise us on the issue at hand. Which means that in order to decide whether or not the ancient Christian churches are actually experts on theology and morality and their adherents should trust them, we would have to have a means of determining what it means to be an expert on theology and morality.
And how would we even do that when we can't trust our own thinking? As famous skeptic Michael Shermer has noted many times and continues to bring forward today, we human beings are notoriously bad at the whole thinking thing, which is why conspiracy theories that require ignoring evidence and assuming that large swaths of humanity are both extremely competent and extremely malicious are still popular across party lines and demographic groups. Even 23% of people with post-graduate degrees are prone to these cognitive errors, which suggests that academic training alone isn't a reliable cure for our normal human cognitive problems. And there's nothing new or interesting about conspiracy theories about religious groups we are predisposed to dislike. Which brings me to the next point...
4. Religion diverts generous impulses and good intentions.
The author is very correct that sometimes religious organizations and religiously motivated charities do enrich their leaders rather than spending their money on more useful projects. That is very true and quite a shame when it happens. It has happened with lots of religious organizations at various times. This claim is true, but misleading because of what it omits. This problem is not unique to those with religious motivations.
While some might think that it is indicative of a problem with religion that a large majority of the scandals around charities come from religious people or explicitly religious charities, that is exactly what we should expect when the vast majority of people are religious. The most plausible explanation for the fact that the majority of charitable misconduct comes from folks with a religious affiliation (in light of the fact that these problems are not exclusive to religious persons) is simply that human beings find it very easy to spend a lot of money on themselves when they have the opportunity.
This is related to a common behavioral problem with human beings, which is that we consume more resources in proportion to the availability of those resources. And this makes perfect sense in light of our evolution under harsh survival pressure, circumstances under which the smart play is to consume as much of a resource as you can while it is available because resources are very scarce and one does not know when that resource might be available in the future.
The author's more specific claims have a somewhat different problem, which is that she assumes that there is an inherent conflict between the behaviors of those who care for another person out of religious motivations and the behaviors that are actually helpful to that person. This might or might not be the case, and we would need an objective morality by which to measure a person's actions in order to adjudicate that claim.
Stay tuned for an examination of the 5th and 6th claims.