The article didn't "attack" atheists. It pointed out that many of the, let's say most prominent people (authors, speakers) of a newer, more forceful atheism are in fact, huge assholes. As you say "atheists" is not a cohesive group, so this fact shouldn't concern the average non-believer much. I read several of the books of these guys in the early 2000s, they were interesting and I think highly valuable. I eventually got bored with it, you can only say "there is no god" so many ways. I never go on board with the whole anti-sjw nonsense either. It is in fact even more boring! So learning that these people who's books I read before are in fact awful people cause my no issue. In fact it's a good lesson!
Obviously atheism is not a religion, so we put no stock in authority, only in the arguments they present. So I can agree with The God Delusion's points, and still find Dawkins to now be an abhorrent scumbag. I used to read Skeptic magazine, but I'm still appealed by Shermer's misogynistic comments, culture war bullshit, and his idiotic libertarian nonsense.