Yes, America discriminates against atheists because atheists are deemed to be people who will never find God. The US is such a religious country that when anyone thinks differently, they are considered strange. An atheist has just as much of a right to believe in what he wants, but that's not how the country views him.
It is my experience that many Americans have more difficulty accepting an individual with no spiritual beliefs than they have accepting individuals with vastly different spiritual beliefs than their own. I recall reading a study in which, presented with an image or scenario or a person performing an unethical behavior, few Americans identified the individual as a Christian, but most were comfortable identifying the person as an atheist, a Muslim, or a rapist. It is also my experience that this discrimination and distrust are unfounded. Atheists often have just as strong an ethical and moral system and just as many values as people belonging to a religion.
If America discriminates against any group, it is against Christians, not atheists. Christians are made fun of all the time. Politicians and government officials make it hard for Christians to practice religion. They make it impossible to even speak about religion at school or in a work place. Atheists on the other hand are a protected group that can offer insults and condescending remarks, without penalty.
Yes, some extreme religionists, primarily Christians, try to spread hate towards atheists for their beliefs. But atheists do the exact same to Christians as a whole, as well as other religions, encompassing a lot of people who do not discriminate against them. It's also important to note that it's not all Christians who do this. In my experience, as a Christian who has never discriminated against any of the many atheists I've met, I've suffered a lot of discrimination and hate from them. There's just as much hate going the other way too.
America as a country accepts all religions. You're free to believe whatever you want. Including atheism. Outside of the independent individuals who do discriminate against atheists, there isn't any. There aren't "anti-atheist rallies" or anything held. In Paine's day, there were far less atheists, but what he said pissed a lot of people off. An atheist who wouldn't say something like that has much less chance of being discriminated against. I see nothing wrong with him stating that. But yes people will get all upset over it. It doesn't show or prove that atheism is some suppressed organization or religion. They have their own places like the church of Satan that they are free to go to. They aren't stopped from their beliefs.
He who denies to another [the right of every Man to his own opinion], makes a slave of himself to his present opinion, because he precludes himself the right of changing it.
I find that even better. Rationality surely is what we should focus on, but we're all just humans who make errors and are also incapable to answer everything logically, so respecting another persons opinion is the most important thing there is.