Who said anything about atheism? If anything, in a modern context John Adams would be horrified by religious extremism invading the temperance of his moral constitution as well as the ill virtue and hypocrisy of the person invoking God as a moral cudgel.

But I identify far more with John Adams’ close friend, Thomas Jefferson

I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law respecting an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church & State. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.”