People on the forums keep saying this, and it bugs me because I think they're largely operating under false assumptions and misunderstandings. While Confucianism is generally not considered a religion, it has functioned historically (and on many other levels) in a way which makes it VERY appropriate to include it in Civ.
To give one example, during the Choson period in Korea (1392-1910), a very strict adherence to Neo-Confucianist doctrine was adopted and propagated throughout the country, creating what in civ game terms was essentially a Confucian Theocracy. During the preceding Koryo period, Buddhism had been held in high regard, on equal footing with Confucianism, one dominating the realm of the spiritual/supernatural and the other dominating the secular/everyday world. However, during the Choson era of Neo-Confucian ascendency, Buddhism and its teachings were ridiculed and attacked by the establishment, with the Confucian principles and practices being held up as the one true and essential doctrine. Though it was an age of great cultural and societal achievement, it was not a very tolerant one. Choson Korea as a nation refused to talk or deal with any other countries besides China, and no foreigners were allowed into the country, nor did anyone go outside of the country -- the rest of the world, filled with heathens, just wasn't Confucian enough to merit dealing with. In addition to the attacks on Buddhism, Koreans who converted to Christianity during this period were also subject to harsh persecution for their deviance from the state philosphy.
So much for existing side-by-side.
Have you ever heard of a Buddhist regime that was that extreme? Or for that matter, a
TAOIST one? How many times has a strict, intolerant Buddhist or Taoist theocracy dominated a nation in such a fashion? I'm pretty sure I can count the number on the fingers of one elbow.
Not that I would recommend removing either Taoism or Buddhism, but think about what religions are in Civ4 and what they represent.