If I were to structure the 'religions' in Civ, I would have started with this extremely rough sketch:
Shamanism
Hindu
Christianity
Islam
Toltec
Buddhism
Ancestor Worship
Greco-Roman Polytheism
Druidic Polytheism
Shinto
Aboriginee
Yoruba (Voodoo is a mix of Catholicism and Yoruba)
And I know I am missing at least one more major African faith
This is very rough though, and about half of these are 'place holders and question marks', where I would want to get a little more education in the given region and then correct them. See my notes below for my thinking at present.
Ancestor worship covers the traditional faiths of the Chinese, Koreans, and those Native Americans who were not Shamanic.
Judaism is not on my list as it is a faith that lacks a missionary aspect. To join it you have to go through an amazing amount of work to prove you are a convert. However if I am wrong on that I would correct this. Further, in the western world despite the lack of a missionary aspect this faith has had an extremely important role, and therefore it might need to be added just to keep things from looking strange to a westerner (and probably 80-95% of Civ IV players live in the western world). Zorastrianism is not on my list as it does not even allow converts.
Other faiths like Shiks, Drew, etc are not on my list as they are too small, but if someone with good knowledge of them could say that they do seek converts I would change this to handle the 'what-if' factor.
However, I would want to sit down and refine my list as much as I could to use general terms rather than specifics where a general term can cover many similar faiths that don't 'fight'. For example, the same term could covers both Christians and Muslims as they are essentially sects of each other, however they are in competitive conflict enough that they can be distinguished. By 5000AD though, it is likely they will be the same religion...
Some of my polytheistic religions might be more justified being grouped together as one, and I would want to sit down and think about that.
Aboriginee might be Shamanic, but I know so little about it that for now I kept it seperate. For all I know it belongs in the same category as 'Greco-Roman', as in that is how little I know about it...
Buddhism has become so intertwined with a pack of 'Buddhist saint-deities' in the eastern countries that it belongs as a religion where other philosophies (such as Taoism) do not (the Taoists who call it a religion are in the extreme minority of Taoists, whereas the opposite is true of Buddhists).
Toltec is a 'place holder' for the faith of the people from the Aztecs down to the Inca. I know for a fact that the Inca and the Aztecs had very different faiths, so this is merely a place a holder until I figure out where to put them each and where to put the Maya on my lists without making my lists grow to big...
Yoruba is a traditional faith of west Africa, and the only such faith whose name I know. For now it is a place holder for 'African religions', but I am sure that keeping things that way would be quite offensive. I don't know enough about the other faiths of Africa however...