The way The Atheist Advocate puts it in the comments, the "persecution" is the use of "schoolyard tactics" to abuse atheists at work (especially in political or judicial positions) or keep them from getting the position or keeping it in the first place, having religious messages in public or on money, and religious folk coming onto his page to preach to them or demand answers for why they're atheists (which he compares to an atheist walking into church and criticizing everyone for being there; not a bad analogy, seeing as how web pages are the closest thing atheists have to a place to congregate).
While calling it "persecution" is a bit heavy-handed, he does have a good point. I'd imagine that anyone who willingly walks out in public in an Atheist shirt, especially if you live in the South or anywhere notably religious, would at least face a lot of questioning and proselytizing. Unfortunately, it seems like a lot of the problems religious folk have gotten with atheists stems not only from their own beliefs, but also the tendency for asshole atheists to act superior and treat anyone with religious beliefs as sheep or terrified cavemen. It doesn't exactly paint a good picture of them.
