If I recall correctly (someone please correct me if its not the case), it wasn't so much that Amaterasu was the main divinity of a well established pantheon. Rather, it was the deity of the clan that would eventually become the Imperial family, as such it was "promoted" to the central place it occupied afterwards.

At the time when the Imperial system was starting, shinto wasn't really a defined thing that some families would believe and others wouldn't. The different clans had "family gods" (ujigami). The struggle that appears in the Kojiki (8th century) between Amaterasu and her brother Susanowo, where they try to decide who is the stronger of the two and he is later exiled, has been interpreted as the allegory of the fights for power between two such clans, for example. Possibly if Izumo, the land that claimed Susanowo as their kami, had won in the power struggles, Amaterasu would have taken a secondary place.