In my view there are two sorts of atheism: the classical or pre-quantum atheism, and the post-quantum one.
The classical atheism (for instance Karl Marx’ “historical materialism”) is based on “scientific materialism” and argues that the space-time continuum (“matter”) is the substrate for our existence. This “materialism” was tricky because we all intuitively tend to consider space-time as a continuum substrate. Christianity was able to overcome this materialism because “by faith we understand that the universe was formed at God’s command, so that what is seen was not made out of what was visible” (Hebrews 11:3). By contrast “classical deterministic science” reinforced it. Now classical atheism is old-fashioned because it clearly conflicts with today’s quantum science.
The post-quantum atheism cannot deny the outside of space-time and therefore the spiritual realm. And since by acknowledging this realm one is led to acknowledge God, this atheism tries to escape this conclusion in two main ways:
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Referring to the outside space-time as “Nothing”. It is the atheism of people like Lawrence Krauss, who invoke quantum physics to claim that the universe comes from “Nothing”. His argument amounts to give God the deceptive Fake Name: “Nothing”, similarly to Odysseus who called himself “Nobody” to deceive Polyphemus.
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Introducing the Multiverse: However this is self-defeating in the end because one acknowledges that there are realms of existence that are not accessible to our senses. And this is the same as acknowledging that there are beings existing outside space-time, or in other words that the parallel worlds are worlds existing in God’s mind.
So these arguments are not arguments in favor of atheism but rather in favor of the existence of God.
If atheists do not accept their own free will and personal identity, then you cannot prove them wrong. These two principles are the basis of any knowledge, and in particular science. If someone doesn’t accept free will and the spiritual component of human beings you cannot prove him/her wrong because the very notion of proof disappears. But then one cannot take anything seriously, in particular rights, and this attitude may become dangerous if it becomes generalized.
By the way, my argument amounts to say that my personal identity is warranted neither by the continuum space-time nor my consciousness. Thus to warrant it an always conscious and enduring being is required, that is, a being who can uninterruptedly claim “I AM” (in Hebrew “YAHWEH”). It happens that this is the Name the God of the Bible claims to be His name. So the God of the Bible is not a Premise but the Conclusion of my argument.