How can both of these facts be true at the same time? I think there are a couple of things to consider here. The first is that in a hugely popular religion such as Christianity, it works perfectly well for most people to believe everything they were taught without any real critical evaluation. There are 2.3 billion Christians in the world, so if only 5% of them significantly alter their beliefs, and only 0.01% of that 5% gain enough of a following to form a new sect, that would still be 11,500 new versions of Christianity in the current living population alone. All it takes is a few people who are willing to change their religious views, and we get endless variations on the same basic framework.
So what is it that drives this huge and ever-increasing level of religious diversity? One major factor is that societies and cultures change over time. A few hundred years ago, almost all Christians believed that God created the universe in the manner described in Genesis, and that homosexuality was an undeniable evil. Today these views are being steadily eroded as people realize that there is abundant evidence for evolution and that there's no reason to condemn gay people. This is not a new phenomenon, either: a while back I summarized Bart Ehrman's description of how early Christianity evolved. Jesus went from preacher to Messiah to God incarnate, Jews went from comrades to Jesus-killers, and the concepts of heaven, hell, souls and the Trinity arose.
Not only do cultures change, but Christianity is introduced to entirely new cultures as well. Missionaries purposely frame their doctrines in terms that the natives can identify with, and the natives often combine Christian beliefs with their existing ones rather than just replacing them. There's even a name for this process: syncretism. Vodun in west Africa, Rastafarianism in Jamaica, and the Unification Church in South Korea are just three examples of this.
The other crucial factor to consider is the remarkable vagueness of holy scriptures. Texts such as the Bible appear to offer great insights into the nature of the universe, yet they are so open to interpretation that readers can come away with any lesson they want. Contradictions and internal conflicts in doctrine, far from being fatal to religion, are in fact engines of religious diversity. Is God a vengeful being who is pouring out his wrath upon humanity, or a kind and nurturing one who is constantly blessing his beloved creations? It depends on which biblical stories you emphasize. Homosexuality is condemned? Not if you interpret every single passage that mentions it in just the right way. The Genesis account of creation is demonstrably wrong? No big deal. Just call it a metaphor and the problem instantly vanishes. The Bible and other religious books can be made to support any virtually any view with enough creative interpretation.
The question of what religious sects manage to survive is a simple matter of natural selection. Those ideas that can appeal to the contemporary culture are the ones that survive, while outdated ones are left in the dust. The Puritans were a significant faction in the early 1600s, but nowadays their name has become synonymous with self-righteous moralizing. In modern times, televangelists like Joel Osteen have become popular by preaching prosperity theology, which essentially says that God wants you to be rich. Early Christians would have been horrified at their line of thinking, but it fits America's consumerist culture like a glove. It's not truth that determines what religions become popular: it's suitability to the current environment.
This dovetails with another, related observation: truth converges, but religion diverges. When arriving at truth in areas like science, people independently reach the same conclusion. But religion is the opposite: it continually branches off of itself like an ever-expanding tree. There's no chance that religions will ever converge upon a single specific conclusion, because they thrive on faith, personal revelation and creative interpretation of scripture rather than evidence and logical argument. Religion is a flat-out terrible method of determining what's true.
These characteristics of religion—subjective, shaped by natural selection, endlessly diverging in every direction—do not in themselves show that religion is false. However, they're precisely the opposite of what we would expect to find if one or more divine beings were guiding everyone toward enlightenment. If the gods really want to lead humanity to a single transcendent truth, they're doing a remarkably bad job.