You are missing a lot about what babies can and cannot do. A baby, for example, can be demonstrated to suppose that a thing before it will remain before it. Try putting a cookie into a cup in front of a baby (or a chimpanzee) using a magician's palm so that the cookie doesn't actually go in the cup. The baby (and the chip) will be very obviously surprised when you show them the empty cup.Babies aren't capable of holding any sort of "isms" at all. Atheism does not mean incapable of forming or holding beliefs. That's what you have to make it mean in order to claim a baby is an atheist. Same with cows, dogs, cats, trees, and so forth. Words like theist and atheist cannot be applied to them, any more that words like patriot, or traitor, believer or non-believer, faithful or unfaithful. These only come online when the brain has had time to develop to hold the capacity for points of view to be held cognitively.
More importantly, you left out the part about what points of view are actually presented to the young brain -- and what that brain will then tend to believe. You can separate twins at birth, and teach them wildly different cultural norms -- and they will not recognize their kinship at all. The points of view they hold cognitively are those they were taught, not those they absorbed from thin air, nor those they were predisposed to learn.