It really, really annoys me when fundamentalist Christians insist that they're being persecuted in this country just because they're not allowed to proselytize in public schools or because someone wishes them a happy holiday instead of a merry Christmas.
And especially in small rural towns, anti-atheist bigotry can turn truly ugly. Being an out atheist means risking ostracism and worse. Out atheist teenagers have been kicked out of public school programs, and then kicked out of public school. Out atheists have been the targets of vandalism and death threats. Even believers can be targeted with anti- atheist ostracism, threats, and vandalism, if they're perceived as being atheists because of their stance on separation of church and state (such as the anti- intelligent- design activists in Dover, Pennsylvania).
And I'm just talking about the U.S., where atheists are, at least in theory, guaranteed equal protection and freedom of non-religion under the 1st and 14th amendments. I'm not even talking about overt theocracies, where denying the existence of God will earn you a death sentence.
If you are a Christian in the United States, then -- when it comes to this particular area of the "privilege/ marginalization" palette -- your Christianity puts you squarely in the "privileged mainstream" category. Christians are in the clear majority in the United States, and they are in the clear mainstream of politics and culture. You're not being thrown to the lions anymore. You haven't been thrown to the lions for almost 2,000 years. You are in the group that is running the show.
C.S. Lewis once said something to the effect that he had more in common with an honest atheist than with a self-righteous, unthinking Christian --- and I agree.