The history of individualism is quite complex. But one of the interesting things about individualism was that it developed partially in tandem with developments in christian doctrine.
A modern "relic" of this is the idea of having a personal relationship with god. This is about as individualistic as you can get: everyone has their own, individual, personal connection. But at the same time, this idea involves the celebration of a deity.
So no, I don't think it's fair or accurate to say that individualism and the belief in deities are incompatible. Furthermore, even if we assume that all "ancient cultures" believe in deities, I don't see how anyone can argue that this belief stems from a lack of individualism, given the history of the concept.
Some interesting sources on the subject (I haven't read all of them, but they all look interesting):
Dumont, L. (1986). Essays on individualism : Modern ideology in anthropological perspective. Chicago: University of Chicago Press.
Morris, C. (1972). The discovery of the individual, 1050-1200. (Church history outlines, 5). London: S.P.C.K. for the Church Historical Society.
Schooler, C.. (1990). The Individual in Japanese History: Parallels to and Divergences from the European Experience. Sociological Forum, 5(4), 569–594. Retrieved from http://www.jstor.org/stable/684686
If you want something that's available for free online, again, my blog post is a good way to start.