I've read the whole thing a number of times now and quite frankly I think its a poor analysis of the video in question that makes a number of assumptions and inferences that are inaccurate and do not address the key points raised.
The main areas I have an issue with (not all of them by any means are):
"First, given what Stephen Fry believes about life, the universe, and everything, why does he even have a problem? If all that is, is the result of blind chance, an impersonal materialistic universe that just ‘happened’, then what’s the problem of suffering children? What is suffering? Why care? The weak die, the strong survive, the species carries on – the categories of ‘wrong’, or ‘injustice’, or ‘evil’ have no place."
This falls into the assumption that atheists are quite happy to accept suffering as a part of the everyday and just 'happens and what's the problem. Now not only is it an inaccurate assumption to make on the part of any atheist, it also ignores the fact that Fry is a Humanist and strongly supports and works towards ending suffering.
"Please, please, please note what I am NOT saying – I am NOT suggesting that people who do not believe in God are not good, or loving. I take it as an empirical fact that many who don’t believe do, to an embarrassing degree, far excel the church in charity, generosity, and love. What I am saying is that without God, there is no way of accounting for why we even care."
So aside from the first and last sentence contradicting each other, this assumes that for a moral code or empathy to exist one needs God. Quite simply that is a claim not supported by a massive body of evidence.
"As a child needs to be lifted onto her father’s lap in order to slap him in the face, Stephen Fry needs God in order to say anything at all about the misery of life."
The old 'you have to believe in God to hate him argument' which kind of forgets that Fry is providing an answer to a hypothetical question.
"In the video, Fry claims that his atheism not only promotes unbelief in general, but also seeks to question what kind of God God might be, given the state of things. "
And yet again forgetting that this is an answer to a hypothetical question.
"Christianity takes suffering very seriously. Without entering into all of the debates about free will and God’s sovereign control, the Bible is clear that suffering is not God’s moral fault, but ours."
So it’s the victims fault that they are suffering! I'm sorry but any attempt to justify original sin is simply bronze age tosh used as a control mechanism.
"We are not entitled to know God’s reasons for what he does, and allows. We may weep, and ache, with the question ‘why?’ We cannot, however, demand God’s justification according to our own standards, and consider him guilty until proven innocent. "
Why are we not entitled? Why must it be a mystery that we are not allowed to question? All I read here is 'shut up, stop asking questions and when you die a good God-fearing boy/girl I will take you to the happy place'. Well I'm sorry but I think the questions should be asked, that ignorance is not a virtue, that we do need to look further than the cross and we don't have all the answers we need.
As does Revelations, the final book of the NT is arguably more violent, cruel and bloody that all of the OT combined.