The atman works through the ego self. It has to. The ego has its own take on it and searches for God to protect itself. The ego is the horse riding on which the Self progresses. Salvation and eternity are the carrots for the horse.
Any idea where the ego came from, given that you say it's basically an illusion? The Atman is presumably the greater reality, yet somehow the ego emerges out of this and seems to develop a life of its own (which is why we all become immersed in the web of Maya). I'm trying to give my own impressions of these vague philosophical ideas, and have no idea how good a representation of them they are.
It almost seems like a myth of original sin, except as far as I know, no such ideas exist in Hinduism. And yet the basic idea is we are somehow
separated by identifying the ego as the real self, separated from the Atman or God. It seems in some ways to evoke the need for the sense of Atonement (at-one-ment) which is such a cornerstone of much Christian belief. And just as Christianity is - to me - totally incapable of giving a meaningful explanation as to how this separation came about, the same is true of these Hindu ideas.
Why on earth would such a separation occur? Naturalistic and evolutionary ideas about the origin of the sense of self have no such problems, though it is possible that some of the tunnel vision of our modern life has come about as a result of living in the crowded communities of towns and cities. There may be certain sensibilities which have atrophied in us since the days of our hunter-gatherer existence as a result of this, and in this sense we could possibly reactivate them by a change of life-style. Most of us know this pretty well anyway - a long walk through beautiful countryside can certainly give a different sense of 'self' to the one that develops by being stuck in front of a computer all day working on spreadsheets.
P.S. To tie my last comments in with the observations in NS's original link, some rather simplistic armchair psychologists have tried to epitomise such activities as being processed more by either the left cerebral hemisphere or the right. Thus, in my last sentence, working on computer spreadsheets would be a left-brain activity, whereas the 'widening' of consciousness which might occur during a country walk would involve more activity from the right hemisphere.