It's generally agreed that it was dominated by female deities, but there's two differing schools of thought.
One school says that the many similar looking depictions of goddesses are depictions of a Minoan "Great Goddess," a motherly goddess who held influence over everything from the underworld to the heavens. There were other gods, but she was dominant over them. Her son (and possibly consort), the Divine Child, was a subordinate war god who was a dying and rising god (like Persephone or Adonis, associated with agriculture and the seasons). When Mycenaean culture superseded Minoan culture in the late Bronze Age, perhaps through invasion or perhaps through "natural processes," the Great Goddess was split into different aspects and eventually into entirely different goddesses. Her role with the Divine Child was reversed, so the dying and rising goddesses Persephone and Ariadne are speculated to have evolved from her. Artemis (compare to Cretan Britomartis) and Demeter may also have aspects of her. The Divine Child may have also been split up and absorbed into gods such as Hades, Zeus, and Poseidon.
The second school of thought is more straightforward. Really, there was never one Great Goddess, there were just many different gods and goddesses that some modern scholars have conflated together. In any case, there's definite agreement that certain Greek gods, myths, rituals, and festivals definitely originate from the Minoans. There's a lot of controversy involved. People have tried to interpret art from the Minoan and Mycenaean from a perspective assuming that classical Greek mythology is a later evolution. Beautiful Minoan art inspires the imagination and draws you in. Interpretations are tainted by people idealizing Minoan civilization. People like the idea of a pantheon dominated by an almighty female deity. There was a big push in a feminist school of anthropology to argue that Minoan culture was a more matriarchal one that was replaced with the patriarchal Mycenaeans, the power of the Great Goddess, and Earth mother, being stolen and given to a male sky deity. The myth of the Minotaur is interpreted as an allegory for this, almost like propaganda. Ariadne is identified as the original Minoan goddess, the myth stripping her of her power and only becoming divine because of Zeus. She is a traitor who meets a tragic end in any version of the story. Minoans seeing the bull as a sacred animal is warped into bestiality and monstrosity. Theseus symbolizes the overthrow of Minoan rule, embodied in the cruel Minos, and the dawn of Greek domination. It's a tempting interpretation for sure.