Part II: This is the classic strawman section. I actually agree with the author that many of the examples given in most debates are evidence of the evil of men, but he fails to recognize that religion has historically provided cover for those actions. Slavery has historically enjoyed such cover. Misogony and homophobia have luxuriated and continue to luxuriate under such religious cover.
I'm quite familiar with the problem of evil and the author did absolutely nothing to negate this. If God knows that evil is happening every minute of the day, He either can do nothing to prevent it or doesn't care to. As Sam Harris points out, God is therefore either impotent or evil. Every day I hear from religious people who claim that God helped them in some manner. They regularly give Him praise for things that He does on their behalf. I find this to be narcissistic, callous, and completely immoral when I consider that at least a dozen children under the age of 5 will have died during the course of you reading my remarks here. They and their parents will beseech Heaven for food and water and this same God who answers frivolous prayers somehow finds these starving children unworthy. There is nothing humble about this line of thinking.
I fail to see how the fact that our holy texts (regardless of how they have been translated or cobbled together) have frequently been shown to be incorrect is a flawed argument. An omniscient being should be able to explain in unambiguous terms what it expects. No holy book fits that description. Whether it is stopping the planetary motion of either our sun or our planet for 24 hours to allow Joshua to finish his battle (Bible - Joshua 10:13) or Muhammad splitting the moon (Qur'an - 54:1-2), these are cosmological claims being made by our religions. I fail to see how my inability to read it in Arabic somehow makes this scientifically possible.
If there is a conflict between religion and science, I get the feeling that the author feels it's ok to reject the scientific account. The problem I have with this is that unlike religion, science is not subjective. It has been the most consistently reliable way for us to determine fact from fiction. When a religious person disputes evolution in favor of creationism or asserts the historicity of a prophet flying to Heaven on a winged horse, those are anti-scientific views. Plain and simple.
Part III: This section basically deals with the author's desire to treat other peoples' beliefs as sacred. As H. L. Mencken said, "We must respect the other fellow's religion, but only in the sense and to the extent that we respect his theory that his wife is beautiful and his children smart." What the author fails to understand is that beliefs directly influence our actions. If the creator of the universe commands us to kill people for imaginary crimes like witchcraft, should we respect that belief (FYI - witch burnings still happen in places like Kenya)? If someone wants a religious belief like creationism taught alongside evolution in our classrooms, is the appropriate response one of tolerance? Unlike Jesus, I don't think we should enact thought-crime legislation, but if religious people cannot keep their unsubstantiated beliefs in check, we must oblige them to.