There are multiple theories, but they all could be true at the same time.

>Cosmic rock that the Syrian Arabs and the Arab Syrian Roman Emperor Elagabalus worshiped
>A symbol of the temple/foundation stone in Judaism that relates to temple worship and church/mosque building in Freemasonry, that also correlates with Neoplatonic sacred geometry, and possibly even alchemy.
>Served as a temporary symbolic temple replacing the destroyed one, with the Dome of the Rock serving as the new one. The real goal of early Islam was just to capture Israel from the "infidels", sort of like a proto-crusade.
>There were multiple Kaabas, and the other ones were destroyed during the Arab civil wars.