Atheists are persecuted far less than Christians are. The worst things that can happen to an atheist in a Christian environment (which is rare) is feeling a little uncomfortable. I feel uncomfortable when being among atheists or other people who are comfortable with their sins and don't believe in God, but you won't see me complaining. There is freedom to practice any religion in this country, so long as that religion does not break any laws of the government. I think separation of church and state (which isn't a law, contrary to popular belief) is fine, but the truth is that a lot of our laws are ultimately based on commandments/principles in the bible. You may not agree with that, but at least show some respect for that fact.
Even if Christians were 90% of the population (and in reality, I think less than 10% are actual Christians, and the rest are nominal) you would not see persecution of atheists. God never says in the Bible to "smite those who do not believe", but rather to show the love, forgiveness, righteousness and compassion that Christ showed, even to towards those who "spitefully use" us and "persecute" us. If, however, the country was 90% atheist, I think that there would be persecution of Christians who truly follow Christ. Already there is an increasing attitude of hate and resentment of Christians in this nation, mostly whenever we Christians speak up against what we believe is wrong. You only need to look at countries where Christians were a small minority in a nation that encouraged atheism to see how Christians have been killed because they stood up in the name of Christ. To this day there are thousands of Christians being killed a year, mostly by people of other religions, but also by atheists. It doesn't take long for resentment to turn into full blown hate and persecution.
There are (perhaps a small number, but a few nonetheless) people even on AT that think that the United States would be better off without Christians, and, were it possible to get away with it, would like to see us Christians all dead. Those who actually preach "tolerance" (which is actually a codeword for "I want to do whatever I want to do, whether it's right or not") don't want to tolerate Christians because they think we are intolerant. And that is true, to an extent: Christians shouldn't tolerate sin. There isn't freedom in sin, like people seem to think; sin actually enslaves and undermines the security and stability of the entire nation. Laws aren't there to control people, but to provide safety and freedom within the law. Christians should hate sin, but show love towards those who commit sin. Hate sin, not the sinner. Hate crime, and justly punish crime according the the laws that are in place, but do not hate the criminal.
It's your right to not believe in God, but don't try and legislate any reference to Him just because you feel uncomfortable about it. This nation has never forced people to worship God, and (hopefully) it never will.