Interesting article, written from the heart. My take is that I feel all those things (samples below) without religious faith. If 'faithful' people think atheism lacks all this, it's no wonder they seem afraid of atheism.
When I told my parish priest I was no longer a christian (i.e. had no religious faith), he said I was "taking the easy way out". He could not have been more wrong. Having no religous faith has not made my life less rich in the kind of feelings described in the article.
"elusive experience of wonder and mystery"
"[Have you] never felt overwhelmed by, and in some way inadequate to, an experience in your life, have never felt something in yourself staking a claim beyond yourself, some wordless mystery straining through word to reach you?"
(not sure what he means by "straining through word"; I can guess, but...)
"moments of wonder and clearest consciousness, which suggested a dimension of existence beyond the everyday"
(I just don't call that dimension god)
"Religion is what you do with these moments of over-mastery in your life"
(Same could be said of scientific enquiry)
"[Faith is] a state of motivation, a desire to reunite with that glimpsed moral beauty and incorporate it into everyday living."
(Moral beauty is equally available to atheists, as is trying to incorporate it into everyday life).