Atheism is a positive statement about the non-existence of invisible Personal causes producing the phenomenal world. In pre-scientific thought there was no division between "natural" and "supernatural" and all the World's phenomena were produced by Agencies that were akin to human beings - they had will, thoughts, and could be communicated with and appeased. The phenomena associated with a particular 'god' came about because that 'god' was present in the phenomena. People experienced the gods through their real effects in the World.

Gradually "naturalism" or "physicalism" - the idea that the world is produced by impersonal processes/substances without human characteristics - replaced the 'gods' as causal forces in the World. Mechanism - the view that Nature is analogous to human-made machinery - gradually moved the 'gods' further and further away, and replaced them by 'matter', a neutral substance that doesn't respond to mere thoughts, prayers and rituals. The World was depersonalised and the 'gods' became invisible. Because naturalism/physicalism/mechanism explain the world so well, the role of the 'gods' became more obscure and harder to pin-point.

Thus 'atheism' is the logical outcome of the success of scientific explanation.

However we still relate to the World instinctively as if it is personal and so people still find 'God'/'gods' meaningful when talking about the World's processes. We can either view that as mere mental habit, or we can talk it as a sign that in some meaningful way that the World is a Person, just as we are, even thought we're apparently composed of matter etc. A lot of mystical discussion replaces the term 'Personal' with 'Spiritual' - but not necessarily as something non-physical.

I think Spirit is the Personal flip-side of matter, but that's just my intuition on the matter ;-)