I think there are two sources of disagreement:
1) Jesus taught principles, not laws. He thought we should love God and each other. Mat 5 reinterprets several of the 10 commandments as focusing on intent. As a result he simply didn't answer all the specific questions we might like him to have answered. Churches make different decisions on things like baptism, both decisions intended to honor God. I don't see anything wrong about this. Where the problem arises is when people claim that their decision is the only one possible for Christians, and this is used in a way to isolate people.
2) Jesus was a radical. There's a tendency for movements started by radicals to lose the radical vision and turn into something more systematic, that captures some of what the leader taught, but missing something of the spirit. That happens at time in Christianity. Not that Christ is missing, but that the message turns in part into legalism. But since Jesus himself wasn't legalistic, the legalistic versions aren't entirely based on his teaching. As such, there are multiple versions.
Christianity is certainly not the only area that's like this. There are many approaches to parenting a child. There are different approaches to treating illnesses. Yet a child is better off with their parent, even if a different parent would do things differently, and a patient is better off being treated by a doctor, even if there are different approaches. Of course there is genuinely bad parenting and genuinely incompetent medicine. So there are limits. But the limits are wider than many Christians believe. But you can''t just sit off on the side and not do anything. You're better off to commit to a solid approach, while respecting people who follow other traditions.