If, at the beginning, the player is weak, infighting and balance of power between AI empires would take priority over investing resources to wipe out the small player empire.
The player isn't much of a threat, and brutal aggression can have severe diplomatic consequences.
Imagine more rational counterparts of European powers in 1939: the player can be more or less like Poland (or a more peripheral place like Norway), but Germany wouldn't be strong enough to believe in successful world conquest, and invasion attempts would earn them momentary expansion followed by crushing defeat.
Another historical reference: the expansion of the Roman republic and empire due to the high fragmentation of other powers and its inclination for relatively peaceful mergers rather than destruction and extermination. How compatible are alien races with each other?