It was goddesses all the way. If the theories like homogenous society is correct then we should not find any other forms of worships. I have stopped believing phallus(linga) and yoni were part of that civilization. However, it is possible that phallus worship and yoni were part of that civilization if we find evidences that the civilization was spread to North-East too. The major reason for me to reject linga worship as being part of that civilization is the realization that the original South Indian society never worshipped linga or yoni. Our goddesses were never worshipped as a symbolic yoni just as Indus valley. Therefore, I believe all the speculations about phallic symbols or Pashupata like figurine(I have read articles where that stone engrave was directly named as Pashupata!) are baseless.
Austro-Asiatics and linga/yoni:
The people who worshipped linga and yoni in Indian subcontinent were Austro-Asiatics like Khasis, Garos and Nagas. However, their main male lineage is East Asian Haplogroup O. There is one exception. The Lodha tribe in Orissa. They do not carry single East Asian lineages and all their lineages are part of Indian set of Haplogroups. Their male lineage distribution is given below.
From the data it is clear that many of the present day North-East(Kashmir + Ganga belt) were speaking Austro-Asiatic languages until the advent of Gauda languages(I will use Gauda languages to denote Indo-Aryan or Indic languages. The word is picked from "Pancha Gauda Brahmana" which was used to denote Northern Brahmins in contrast to Southern Brahmins who were known as Pancha Dravida Brahmana). A member at Quetzalcoatl anthropology forum speculated there could have been a civilization of Austro-Asiatics. A reader commented previously that South Indian linga worship was mostly derived from Kashmir and Central East Indian traditions. So no more discussions about Kashmir Pundits and Konkani Saraswat Brahmins as both seem to be part of Austro-Asiatics. It looks like most of the Dravidian sounding surnames of Konkani Saraswat Brahmins might be due to their a millennium long association with Kannada kingdoms as Goa was part of many Kannada kingdoms(The kingdoms that encouraged Kannada language and culture).
This article describes the linga/yoni worship among North Eastern tribes.
The manner of worship:
Unfortunately, we do not how those goddesses were worshipped. Is it some kind of ritualistic worship or spirit worship? Tulu/Malayala goddess worship is primarily spirit worship. There are three types of spirit worship in this region.
1. Goddess worship
2. Spirit worship(all kinds of spirits, animals, region specific spirits, heroes and even few Hindu gods)
3. Serpent worship.
In all these, a Paatri or a Koraccha or a Belicchappad would get possessed by the respective spirits and go into trance. Those spirits then would talk to people thro' this oracle. Mostly, these priests were non-Brahmins but there were exceptions. During serpent worship in Tulu regions the Paatri was generally a Brahmin.
However, spirit worship is observed in North Indian society too. According to a member at Quetzalcoatl forum, in Uttaranchal during Dasara there is a day when a female go into trance possessed by a spirit. Even in Maharashtra (again during Dasara) few Brahmin females become Paatris. However, I am not sure in either cases whether they say the futuristic things to the devotees. It is interesting that in both cases it is females who act as oracles. Since Indian female lineages are mostly unchanged across castes and tribes probably their religious practices might give the origianal form of worship in Indus valley. However, in South India all the Paatris are males. This is an anomaly in a matrilineal society when patrilineal North India still have female Paatris.
How men became Paatris?
While growing up in my region it was common to hear rumours like somebody getting possessed (the goddess(amma) has possessed her, they would remark) and that somebody would always be a woman(though, even if some males also got possessed that won't make much difference to my arguments). I wonder the reason behind that. Were they faking it or was it some kind of psychological disorder? I don't know. However, I can see a clue for males to become a oracle in that phenomenon.
May be sometimes those possessd females would speak uncontrollably and do some extraordinary/abnormal physical activity(biting chicken?). This would drive others into some kind of shock and fear. Some men might have used this. Probably, those females who go into trance might be due to some unknown reasons but males started faking it. Thus born Paatri. Mostly these men became very successful in controlling the masses. Over time few smart women might have understood it and they too have started faking it. Probably, in North India we still have few such women.
I came across a reference that Burushos were basically Shamans at Quetzalcoatl anthropology forum. I wondered about differences between Shamanism practiced by Burushos and Tuluvas. One of the members mentioned that Burushos' bite a chicken during the ritual. Well, Tuluvas too have exactly the same procedure during "Bhutada Kola". Now let's make Tuluva, Burusho connection.
|_________Turvasha_______Turuva_____Tulu(Enemy of Aryas)
Let's check male lineages of Burushos(Sengupta et al. 2006, again thanks to Haplogroup R2 friend).
Burusho Haplogroups fall into South Asian male genetic lineages. However, such a large Haplogroup R* looks suspicious. Unfortunately, we don't have Tulu male lineages.
Roots of various gods/goddesses in Hinduism:
Austro-Asiatic : Linga and Yoni (Shiva and Shakti)
Dravidian/Indus valley: Goddesses
Semitic/Elamite: Brahma, Vaivaswata Manu, probably Vishnu(Rama and Krishna)
Vedic: Indra, Agni, Vayu etc..
Of course, most of these are unrecognizably mixed in Hinduism.
I was trying to find a connection between Elamites and Dravidians. Didn't find any. I suppose Elamo-Dravidian linguistic family has been discredited. I thought I saw something when I read somewhere that the heir apparent of Elam kings was always "son of the sister". I thought I found something here as it was the case with Tulu/Malayalee rulers too. However, another article corrected it and said it should be read "son with his own sister". Probably, this still gives clues for matrilineal traditions and also cross-cousin, uncle-niece marriages practiced in South India. Probably, all started with that incestous relationships but the inheritance pattern remained unchanged even after brother-sister marriages vanished.