How many citizens follow a religion depends on how much pressure has accumulated in a city. There is also a pressure for atheism, I'm not 100% clear on where it comes from, but it counts a religious influence. A missionary or prophet spread adds 1000 influence of its associated religion. Prophets and inquisitors remove all influence from all religion but their own. Evangelism removes 25% of the influence of all other religions.
Later on in the game, when cities have thousands of influence accumulated, a missionary adding 1000 for your own religion doesn't really tip the scale much. It might only convert one or two pop. But by removing say 800 influence from every other religion, your religion now has a much better ratio of influence, so more pops are converted. Your missionaries are better at converting cities with established religions. So if you have been buying and settling alot of prophets, you have a cheaper way to convert other civs than buying several prophets, which increase in cost for ever one purchased.