In most mythologies, there is often a male god who is the chief god, like Zeus of Greek mythology and Ra of Egyptian mythology. As far as I know, the only mythology that has a female ruler of the universe is Ameteratsu, the Sun goddess of the Shinto pantheon/Japanese mythology. Are there any other mythologies that have goddesses as the main deity as well?
I take this question to refer to the chief deity of the “day to day” pantheon. Many religions have primordial goddesses that are arguably older and more powerful than the deities that are the object of day-to-day worship, but were supplanted (like Gaea) or are rarely referenced (such as Nyx).1
Likely reflecting the male-dominated outlook of many cultures, most such chief deities are male. However, some are female. Besides your example of Ameteratsu, I can think of a few others:
In Odinani religion, the primary deity is Ala. The true supreme deity is Chinukwu, who generally seems to be genderless, but is not worshipped:
Chukwu is genderless and is reached through various spiritual forces mainly under the spirit class of Alusi who are incarnations of the high god; no sacrifices, however, are given to Chukwu and no shrines and altars are erected for him.
Ala is female, and chief of the gods who are actually worshipped:
Ala (meaning ‘earth’ and ‘land’ in Igbo, also Ájá-ànà) is the feminine earth spirit who is responsible for morality, fertility and the dead ancestors who are stored in the underworld in her womb. Ala is at the head of the Igbo pantheon, maintaining order and carrying out justice against wrongdoers. Ala is the most prominent and worshipped alusi, almost every Igbo village has a shrine dedicated to her called íhú Ala where major decisions are taken. Ala is believed to be involved in all aspects of human affairs including festivals and at offerings.
In fact, the very name Odinani appears to contain a derivative of “Ala.”
In Winti, Aisa is another supreme earth goddess:
Aisa(eye sah), mother god of the earth, is the highest and is considered closest to Anana. Which is why at most Winti rituals or payers begin with an offering or odo(oh doh) to Aisa, hoping that she will intervene on your behalf regarding many issues, such as healing, protection, or general blessing.
There is also a supreme deity, who may be male or genderless, but (as with Ala) Aisa is the chief divinity of the pantheon.
1: That Nyx was of comparable power to Zeus, or greater than him, seems quite likely. In the Iliad, Hypnos makes reference to a previous instance in which he had aroused the wrath of Zeus, and fled to Nyx for shelter: “To her I came in my flight, and besought her, and Zeus refrained him, albeit he was wroth, for he had awe lest he do aught displeasing to swift Night.” She is also referred to as “Night that bends to her sway both gods and men.”
I'd offer that the ancient Celtic Gods of the Tuatha dé Danaan were another. From the wiki page:
"In Irish-Celtic mythology, the Tuatha Dé Danann ("People of the goddess Danu") are the Irish race of gods, founded by the goddess Danu. These gods, who originally lived on 'the islands in the west', had perfected the use of magic."
A European example is Basque mythology, at least probably.
Some say the goddess Mari in leads the other deities, or that she is the most prominent mythical being in Basque tradition, but little is known about her consort Sugaar (Maju). Interestingly in Basque mythology both Sun (Eki) and Moon (Ilazki) are female.