The persecution of Christians
It is perplexing to say the least that the Church itself should be guilty of persecuting Christians, but the history is absolutely clear. By ruling certain communities of Christians as heretics, they can control the masses by publicly persecuting people who believe different things about the church. The irony is sewn into the church so thoroughly that even today, Christians tend to dismiss Gnostic ideas as "obviously heretical."
The other Gospels
The Bible's canon wasn't set until long after Jesus lived and was crucified, but today, the tone among the Church abroad is that it is obvious and self-explanatory. In reality, there were entire communities of Christians with other books in their Bible, including other Gospels, so that their understanding of Jesus was unique and sometimes very mystic. These other Gospels are ironic for many reasons, not the least of which is that most Christians don't know anything about them.
The esoteric Jesus
In the Bible, Jesus's character is described as an esoteric teacher (for instance, his disciples ask him why he teaches in riddles and parables, because they want him to teach more straightforwardly, but he says, "Those who have ears to hear will hear," in Matthew 13). Yet, as Pagels notes, the Church universally rejected that idea, because like the disciples, they preferred a Jesus who would not teach in riddles and mysteries. The truth is obviously that Christianity is a mystic religion, especially in the communities that were ruled out as heretics.
Church as profitable business
The Church seems like a service, but Pagels offers a different narrative that aligns more closely with the historical findings. Perhaps the real situation is that the early Catholic church managed to eliminate competing churches for their own profits sake. They collected tithes from Church members, so the other churches were literally competition, and through the establishment of orthodoxy, they monopolized the tithe-market.
The current status of Gnosticism
The current treatment of Gnosticism in the eyes of Christians is fairly bad. This is because, ironically, the Church tradition is so powerful that the prejudiced ideas from all that time ago still dominate the Church at large, even across denominational divides. There are almost no churches that accept Gnostic Gospels into their discussions of the Bible. So, if Pagels is right about the history of the early church, the church has done a serious disservice to entire communities of oppressed Christians.