As an atheist, the origins for a persons disbelief in god(s) comes from the same place a persons belief in god(s) comes from. Within the individual.
Myself, I was raised in a baptist home and spent a few years in the baptist children's home as a teen. I fully believed in god at that time and immersed myself in studying the bible morning, noon and night. I studied mainly textual criticisms of the NT but spent a few months looking into why the newly founded christian canon would seek to rearrange the order that the books appeared originally in the Tanakh.
It was during this period that the seeds of doubt started. I was raised that the bible was the infallible word of god and when I started noticing things that couldn't be reconciled I tried every way possible to make them fit together but eventually I had to admit that there was a mistake. This revelation didnt sit well with the whole 'infallible word of god' belief I was taught so eventually cracks in my faith started to form. I wonder how I would have ended up had I been raised in a more apologetic faith that can handle a fallible bible but I dont spend a lot a lot of time thinking about it now. I do still enjoy textual criticism of the ancients texts which is why I spend a lot of time on religiously themed forums and groups so I guess that's a positive.
A lot of atheists will make the claim that we are all born atheist and only find a god after being indoctrinated by our societies. The way I define atheism is making a positive claim that god does not exist or that there is no evidence of such a being. Obviously newborns dont make claims about a lot except that they need a bottle so I disagree with this claim. Newborns certainly arent theists nor are they agnostic. "Unaffiliated" seems pretty accurate. lol. If you define atheism as the lack of a belief in god then newborns do fit that definition and I think that's where the confusion comes from.
In the end, there are those with very low evidence thresholds for things they are willing to believe in and there are those whos thresholds are higher. We see it not just in religion but almost every topic; conspiracy theories, claims of personal conquests, new scientific advances etc. That's why some of us are atheists and some are theists, polytheists, etc.