Here’s one big problem that atheists have with the Bible: they assume the Bible functions as a set of instructions for how to go to heaven. And then they predictably criticize the Bible because, well, it isn’t that.
But don’t blame the atheists: they get that idea from many Christians.
Here’s another problem: atheists expect the Bible should exhibit hallmarks that it is the product of divine discourse, hallmarks that cannot be denied by any rational person. But the Bible doesn’t have those hallmarks. So the atheists proceed to toss the Bible.
Once again, don’t blame the atheists: they also get that idea from many Christians.