When it comes to Bible study, there's a right and a wrong. The Bible can, and should, be studied alone, but the Bible can, and should, be read in a community. The benefit of studying alone is it protects you from erroneous group think, and avoiding denominational bias. The benefit of studying together is it allows a group to pool their knowledge, and correct individual errors.
The problem atheists have is they fail to study in the same manner. Whereas faithful Christians believe this is God's book, and so we have the goal of fully understanding and applying the Bible to the best of our abilities, atheists have no such motive. Thus, they rarely study it, much less with pure motives to understand it. Usually, it's more about making it sound as stupid and/or evil as possible. Thus, atheists are significantly less motivated to take the Bible in context.
When studying alone, it's far easier to take Scripture out of context, but even a study within an atheistic community will fail. See, when Christians study together, we do so with the intention of building each other up. I have a question, my Christian brethren might have the answer. Someone asks me a question, I might have the answer. By studying this way, we're better for it. Gaps in our knowledge are filled, and errors are corrected.
But what of atheists? They typically don't study at all, much less gather together in a community with the intention of spiritual growth and correctly understanding God's Holy word. The majority of an atheist's knowledge usually comes from what they've been told to believe by their influencers. Every popular atheist website I am aware of twists the Scriptures in ways a 5 second Google search could prove erroneous, and in my experience, vocal atheists repeat those claims without stopping to question them.
Of course, with about 500 million atheists worldwide, one cannot speak to all of them. Some atheists may well be both sincere and fastidious in their studies. But it does seem that the majority, and certainly the most vocal, do not even intend to understand the book before criticising it. And so the simple question I ask is why? What is it about Christianity that is so repugnant to you that you would criticise it before you understand it?
Here is the main truth of Christianity: We were created by God, and have rebelled against Him. We deserve punishment for this rebellion, but God is not willing to deliver it. Therefore, God sent Jesus to live as a man, never rebelling against God. And yet, He died as a rebel, receiving the full punishment for sin. After that, He rose. Because of this, all who turn from their rebellion, confess Jesus as Lord, and believe He rose, will be resurrected in God's eternal Kingdom, living forever in perfection. Those who don't will receive the punishment for their own sins.