Well, Kant argued that scientistic, evidence-based rational arguments about God are wrongheaded, but he proceeded to give a pragmatic, moral argument for religious faith.
Atheism may largely derive from hostility, incredulity, disgust, and other negative reactions to religion, but in many cases those reactions are wholly justified. Organized religions are often appalling.
I agree the universe is likely far more complex and mysterious than we can comprehend, and it's that very alienness and inhumanity that are inevitably reflected in our behaviour, when we fail to live up to our ideals. The absurdities of religions and of secular culture reflect not so much the familiarity of an anthropomorphic god or some rational, humanistic script, but the universe's strangeness.