System of a Down - Ego Brain Lyrics Meaning

Ego Brain at the most general level is about how our modern lives are unsustainable, precariously balanced on a system entirely reliant on non-renewable resources. Eventually this system will break down, leaving no replacement for itself.

"Life is but a dream,
Drifting on a stream, a stream,
Consciously it seems,
All of what remains,"

"Ego Brain" itself refers to the self-centered nature of man. "Man made shame, love after it rains" could be referring to the notion that mankind has sown these seeds of destruction, and that no one will care until after disaster has struck.
Because no one is willing to admit there is a problem, life as we know it will crumble. The problem is real, we all know the problem exists, yet we choose to ignore it:

"You see my pain is real,
Watch my world dissolve,
And pretend that none of us see the Fall,"

"As I turn to sand" refers to man's eventual self-destruction.
"You took me by the hand" is an extremely ambiguous line; it most likely refers to a "savior" of mankind, perhaps referring to religion maintaining order when civilization breaks down. Alternatively, "you" could be referring to the main cause of the problem; big corporations, big governments, the "system" which keeps the rest of humanity under their thumb in the name of profits and power. Rather than using that power to avert disaster, they use their power to simply sedate the population for its impending euthanasia, distracting it with meaningless rhetoric, such as "love prevails over all".

"I am just a man,
Fighting other men,
For land, for land,
While I turn to sand,
In spite of the pain"

This passage is referring once again to mankind's destructive nature, this time naming war, rather than over-consumption through rampant consumerism. Despite the destruction wreaked upon not just ourselves but the planet as well, humans have not stopped fighting.

This is a general interpretation of the song, the lyrics may hold completely different intended meanings, or specific passages may hold more specific meaning, referring to specific people and events, but this is what I've made of it.