We don't.

Amen is derived, ultimately, from Hebrew אָמֵן, meaning so be it (essentially) and is rendered in Greek as ἀμήν, whereas Amun/Amon is rendered in Greek as Ἄμμων

Very different words, that just happen to sound vaguely similar.

Amen is a Hebrew word meaning, "truly," or "let it be true." It has no etymological connection to the Egyptian Amun/Amon/Ammon.