On the first point, I recommended this person look up Christopher Hitchens and reconsider whether Sam Harris really is that hostile towards religion in comparison.
On the second point, well, it gets more complicated. On the one hand, I think that Sam Harris has some valid and pointed criticisms of Islam and has made a career speaking publicly about the potential, and in some cases demonstrable, harm which the religion's scriptures and preachments can produce.
For instance, the infamous 9/11 hijacking was committed by the truest of believers, as was the murder of Danish cartoonists and filmmakers, the fatwa on the head of Salman Rushdie for the crime of writing a fictional book, the fatwa on Ayaan Hirsi Ali for leaving the religion and speaking out against chopping off the clitoris of baby girls, the countless and ongoing atrocities committed by ISIS against homosexuals and infidels, the murderous riots which stemmed from an inflammatory video daring to depict the Prophet Muhammad (one of which resulted in the Benghazi kerfuffle), and many other instances of faithful Muslims who take their religion and its texts literally.
The trouble with Sam's view, or rather the perception of Sam's view which I would argue he hasn't done enough to correct, is that these many examples of extremism are not representative of the religion as a whole, in much the same way that not all Christians are responsible for the Crusades, the Spanish Inquisition, the Ku Klux Klan, the Holocaust, bombings of abortion clinics or the murder of abortion doctors. To confound the matter, many misunderstand Sam Harris' criticisms of the beliefs and tenets of Islam as bigotry against Muslim people (see video below).
In a way, and I am hardly the first to make this point, the Muslim world is currently undergoing a series of growing pains similar to Christianity during the Dark Ages. Hopefully more moderate Muslims will win out, as with Christians, but only time will tell. And I think this is Sam's overall point in criticizing Islam. It's not that Islam necessarily results in terrorism. But rather that it's teachings can be interpreted in such a way that terrorism is a result. A Christian example would be how Hitler exploited traditional Christian beliefs and prejudices about the Jews being responsible for the death of Jesus to build his Nazi army.
Likewise, the Bible supports some terrible things as well, such as the subjugation of women, the genocide of various middle eastern tribes, the stoning of homosexuals, apostates, disobedient children, those who work on the Sabbath, those who eat shellfish and those who wear mixed fabrics. If any Christian or Jewish sect followed the Bible literally and enforced these rules--which believers often defend as morally necessary for the time and people of the Bible--we in civilized society would have a moral obligation to stamp it out. Fortunately, however, most Christians and Jews don't take their holy books that seriously.
So when Sam Harris calls Islam "the mother load of bad ideas" understand that he means this in a context in which Muslims take their religion seriously and literally, and that the only real criticism a moderate believer can level against a scriptural literalist is a lack of nuance which all too often is based on an irreconcilable cognitive dissonance in the mind of the moderate. In other words, the reason a moderate is not a literalist is often because taking scripture literally--like when the Bible tells you what is an acceptable consequence for a disobedient slave--conflicts with a person's inner morality. Both are arguing from a position of faith and a presumption of scriptural authority, rather than reason and evidence. Therefore, how can one side claim the other is wrong in any absolute sense?
It seems to me that the best way for Muslims and Christians and Jews to assimilate into a cooperative multicultural society may well be for the growing moderates to cherry pick their respective religious texts and disregard the unpleasant bits. We may in fact depend on this apparent hypocrisy. The trouble seems to come from believing in the inerrancy of scripture. As much as I would like to see religion become a thing of the past, I must admit that a world of self-serving cherry-picking moderates is preferable to a world of valiant idealistic literalists.
BONUS MATERIAL:
Sam Harris calling Islam "the mother load of bad ideas" and Ben Affleck losing his mind: