Atheist Fundamentalism

[Neo-Scholastic]

Atheists often forget the myriad of ways a religion can be followed. NOT extracting your morals from the holy book is the basic lesson of religion - something you learn on your first day.

There is some truth to this idea. Ultimately however morals do not come directly from any sacred text; but rather, from God. God’s influence is not limited to instruction from an inspired text. It can also include providential order in the form of civil laws that enforce moral behavior until an individual can understand and adopt as part of their religious understanding. It also includes a conscience and intellect that can reflect on the previous in the event that the individual has received flawed instruction and/or was raised in a wicked society.

Same with the bible. Nowhere does it say 'this story is allegorical', so how on earth are we supposed to know when talking to a theist what part they accept and what part they reject unless it comes up in discussion?

Sacred texts do not exist in a vacuum. They are nested within cultures and traditions. They are particularly complex and one must receive proper instruction about them in order to make such subtle judgments. Demanding the precision of mathematics is simply unrealistic when navigating through the many and various circumstances of life to which the texts refer. Such a demand by an atheist is just as fundamentalist and literal minded as the believer he condemns. That I believe is the jist of the OP.