There are many reasons.
Jesus said "do not be calling one another leaders, for you are all brothers and sisters. One is your leader, the Christ."
In contrast to Jesus' words, the various "apostolic fathers" all say things like "obey your bishop as if he was the lord" or "those who don't listen to the bishop are forsaking the church" or things like that. (Various translations substitute another version of the word "bishop" but the point is the same.)
The books of First and Second Timothy, for instance, promote the idea that there is some kind of church hierarchy with "elders and ministerial servants" (or "bishops and deacons") but Jesus did not ever say anything about such a hierarchy.
The words often translated from the gospels as "kings" and "kingdom" in the English language translations can also be translated in different ways depending on the context, and don't always have to do with some kind of governing-hierarchy-thing.
Also, after studying kabbalistic literature and gnostic doctrines, it becomes clear when there is a supposed "Bible book" that really is promoting one of those spiritistic doctrines rather than what Christ taught.
Take the book of James, for example. If you read in the Greek Interlinear at James 3:6, the expression "the wheel of birth" is used. That is found in kabbalistic and gnostic teachings. It does not belong in the Bible.
From the time of the exodus from Egypt, there were apostate Jews attempting to mix Egyptian style or other pagan doctrines into their worship. The golden calf incident right off the bat, all those years in the wilderness some were also worshipping the stars as is brought out in the book of Acts, later in Jeremiah and Ezekiel it's clear some of the Israelites were worshipping the Queen of the Heavens...and in Jesus' day he said the scribes and Pharisees were a source of leaven or hypocrisy.
The caretakers of the scriptures throughout the history of Israel were religious hypocrites. They mixed in false doctrines along with the truth that had been written down by Moses. By the time Jesus walked the earth, that hypocrisy was at its peak. The supposed canon of the "Old Testament" had lies mixed in even then.
Jesus made clear that the hierarchical ways of the Pharisees were not God's ways.
The arrangement of going to a synagogue every week was not something Jesus said anyone had to do. In the old Mosaic Law, the people were supposed to stay home on the sabbath and chill out. They had three major festivals during the year. Many of the traditions of modern Judaism or even during historic times in the nation were not things mandated by God. They were added on activities that made things more difficult for the people and were introduced by religious hypocrites.
The modern church structures are the same way.
Ignatius, Polycarp, all those "apostolic fathers" were like the hypocritical Pharisees. They wrote letters and mixed in truth with falsehood, just like Watchtower writers do.
None of the "Paul" books were really written by Paul. The Galatians account of Paul's time learning about Christ and where he went shortly after is in direct opposition to the account written in Acts. A closer examination of all those "Paul" books shows he did not write them at all.
The head covering thing in Corinthians says a woman needs her head covered and a man can't pray with his head covered; and yet under the Mosaic Law the high priest had to wear a turban and he said prayers all the time with his head covered. Paul didn't write Corinthians. It was written by pharisaical types who were mixing kabbalistic style traditions. You can google what kabbalistic traditions say about women's head coverings. It's totally whacked.
Anyway, those are just a few example, but there are a ton more if that's something you want to talk about. I've gone through all the books with a fine-toothed comb, and there are some books in the current "Bible canon" lists that don't belong at all; others have whole portions that are spurious.
