This article is full of nonsense.
For one thing, the group of writers and intellectuals informally known as 'The New Atheists' do not disproportionately focus on Islam. If anything, their works do slightly disproportionately focus on Christianity given that they are all from countries with indigenous Christian cultures.
The only example that this article has actually provided of 'irrationality' is a tweet by Richard Dawkins and a hideous and borderline-slanderous misrepresentation of Sam Harris*. There is nothing of the arguments these people have actually put forward in their works, or the rationalisations they provide for their conclusions.
Incidentally, if anyone wants to hear a response from the other side, you can read a rebuttal written by Sam Harris on his blog here:
http://www.samharris.org/site/full_text/response-to-controversy2/