Part of the point is that the Emperor is also not perfect. He got too full of himself which led to his deification against his will. He was also literally an imperialist and an authoritarian.

As I interpret the lore his intentions were largely noble but his hubris and refusal to acknowledge the existence of the Chaos gods led to the disillusionment of many of his kids/generals, thus leading to the Horus Heresy and the shitty state of the 41st millennium.