Because the definition of "alive" is different than the question implies.
A "living organism" is a group of molecules that function in a group of multiple ways together in one big group to "proliferate"; as in "grow" and "multiply".
By this definition, atoms don't "grow" and "multiply" nor they function in a group of multiple ways when present together.
However, when those atoms stack together in gigantic numbers and form chemically reactive molecules, they start interacting with other similar molecules and give rise to more complex chemical structures that result in even more complex and functioning biochemical structures that sum together into a "living ogranism"
I hope that answers you question. This question is on the "philosophical" side of science. Which is pretty hard to explain.