Understanding atheist mentality is a chore.
I can certainly understand harboring doubts about God's existence; I was an atheist in college (Ayn Rand (de)converted me, I'm embarrassed to say), and until a decade ago I was an agonized agnostic. I converted to Catholicism, for a host of reasons, not the least of which was my realization that much of the atheist/Darwinist/materialist conventional wisdom I had absorbed in college and in the media was rank b.s. The intelligent design movement laid Darwinist mythology bare. I came to see that the story I had been fed (and which I had accepted without question)-- which was that Darwin and materialist scientists had explained the universe and man without any need to invoke God-- was a lie. A transparent lie. And I was very angry.
So I began to take Christianity seriously, but I feared philosophical disproof of God's existence. I still held to the secular elitist lie: really smart people know that God doesn't exist, belief in God is a psychological crutch, ad nauseum. When I mustered the courage to read debates between Christians and atheists, I had trouble reading because I kept bursting out in laughter. Atheists had nothing of substance to say. Their arguments were scattered, reactive, incoherent, often mere crude (and rude) proclamations of scientism. I was astonished, and remain astonished, how little atheists have in their armamentarium. Atheism is a shabby superstition.
The conversion of my heart was (and is) another matter, and took a different path. The conversion of my intellect was complete with my encounter with Aquinas.
But I can sympathize with doubt; I doubted myself, for many years, in part of course because I didn't want to know the truth, but largely because I had been indoctrinated by atheist b.s., and I had come to accept atheist claims uncritically. Once I became a skeptic, I saw atheist mythology for what it is.
But when I was an atheist and an agnostic I was never 'persecuted'. In fact, my godlessness was a social lubricant. I moved more easily in scientific and academic circles via the well-timed sneer at faith. I never, even in my darkest atheist days, felt anything close to persecution. Atheism, if anything, was a ticket to advance.
So I'm astonished at atheists' complaints of persecution. What on earth could they mean? Let's consider:
1) Perhaps a lot of people don't like atheism. This is no doubt true, but having a unpopular viewpoint does not constitute 'persecution'. After all, Christians have been the losers for years on aggressive litigation that has scrubbed mention of God from their schools and from much of the public square. Did atheists really expect us to like Madeline Murray O'Hare, or Michael Newdow or P.Z. Myers? Being disliked by Christians who you've sued, insulted, censored, and generally slammed around isn't persecution. It's the inevitable consequence of atheist tactics. You earned our animosity, guys.
2) Less than half of Americans would vote for an atheist for public office. I certainly wouldn't. I'm sick of hypersensitive atheist jerks running to court every time a valedictorian tries to mention God at her graduation. I'm sick of atheist ideologues dragging us to federal court to insulate their creation myth from honest questions in biology class. I can't impeach the idiot judges who enable this nonsense, but I damn sure can work to make sure that atheists don't hold public office. If you want my vote, respect my freedom.
3) Are atheists barred from the corridors of power? By no means. Atheists dominate the mainstream media, academia, Hollywood, and the upper echelons of science. Devout Christians are so rare in these powerful sectors of our culture that you can name them: Brit Hume, Robert George, Jon Voight, and Francis Collins. Can you name the atheists in these power cliques? Just make a list of all the powerbrokers in these fields, and you've essentially named the atheists.
So are atheists persecuted? Spare me. The 20th century was the apogee of anti-religious violence. The 20th century was the most horrible century of Christian martyrs; most estimates run to 30 million, mostly at the hands of... atheists. Jews died by the millions simply because they were Jews.
So tell me about the anti-atheist persecution, analogous to pervasive anti-Christian persecution under Marxism? Tell me about the anti-atheist pogroms, analogous to the Holocaust? The truth is that in America, and in much of the West, atheism is a career lubricant, moving atheists to the higher echelons of media and arts and academia and entertainment and science. A sneer here, a wry wink there, and you're in the club. Mention your faith, and they want your scalp.
The modest and utterly non-violent anti-atheist resentment that does exist in the U.S. is a reasonable response to a century of atheist assault on Christian culture. Atheists earned it, in spades.