There's something about the internet which brings out the worst in us. Anonymity, lack of responsibility or accountability, lack of a human face to our opponents, plus a certain cocksure-ness that comes from the fact that you can't punch people in the face over TCP/IP: it's like kids teasing a fenced dog or animal at the zoo for no other reason than that it can't get back at them. It's a little thrill of power-over that is foreign to none of us.
Certainly one of the more personally annoying aspects of this is the treatment of religion on the tubes. I was reading two articles on CNN where it got rather bad, but really the same sort of thing happens anywhere religion (and a lot of other topics, as well) gets mentioned--a swarm of ditto-head Internet atheists descends and leaves behind a sprinkling of comments like goat-turds, ranging from calls for church taxation to legitimate (though off-topic) critiques of the irrational manifestations of religion (creationism, PMD, theocracy, homophobia, etc) used to condemn all belief everywhere, and from the odd assumption that all religion everywhere has been proven to be irrational to the utterly naif and rationally hopeless "religion is often used as a casus belli, therefore religion causes more wars than anything else."
It's helpful to remember that 95% of everything is crap; that goes double on the internet. It's also helpful to remember that, with a world population careening towards 7 billion, millions of idiots can be found in support of any given position, regardless of whether that position is true or false. That goes for theism and atheism both. This makes strawmen terribly easy to construct and believe--any argument and position, no matter how demonstrably stupid, will have large numbers of people advocating and believing it, and thanks to the internet they are all at your fingertips whenever you need reassure yourself of just how idiotic the other side is.
I've nothing against unbelief or uncertainty; I've wandered rather close myself at times. It is, however, rather irksome to hear someone making the a priori claim to the rational high ground while prattling on with missionary zeal in a breathless stream of condescending snark towards a strawman caricature of my beliefs, backed up by logical fallacies, unproven assertions, and the occasional correct argument against some nonsense like creationism, by which they seek to cast aspersions on the personal convictions and cognitive abilities of a vocal critic of said nonsense.
Writ large, this is the great failing of the new atheism. The sudden boldness of the non-believers was a reaction--an understandable reaction, perhaps even a necessary reaction--to the geopolitical reality of crazy religious people doing crazy things. I get that; but when they adopted the proselytizing condescension of the religious crazies they were reacting against, whatever good might have been accomplished was largely offset by having to add Richard Dawkins, Christopher Hitchens, and a thousand thousand comment trolls to my List of People Who Annoy Me. Right in there with the Mormons, Jehovah's Witnesses, and the god-awful BCM praise band back in college. Those who set out to tear down religion have become the guy who sits next to you on the airplane and pulls out a Chick tract. Way to be.