That’s not to say that I think everything is within the scope of human knowledge. Surely there are things not dreamt of in our philosophy, not to mention in our science – but that fact is not a reason to believe in supernatural beings. I think many arguments for the existence of a God depend on the insufficiencies of human cognition. I readily grant that we have cognitive limitations. But when we bump up against them, when we find we cannot explain something — like why the fundamental physical parameters happen to have the values that they have — the right conclusion to draw is that we just can’t explain the thing. That’s the proper place for agnosticism and humility.
But getting back to your question: I’m puzzled why you are puzzled how rational people could disagree about the existence of God. Why not ask about disagreements among theists? Jews and Muslims disagree with Christians about the divinity of Jesus; Protestants disagree with Catholics about the virginity of Mary; Protestants disagree with Protestants about predestination, infant baptism and the inerrancy of the Bible. Hindus think there are many gods while Unitarians think there is at most one. Don’t all these disagreements demand explanation too? Must a Christian Scientist say that Episcopalians are just not thinking clearly? Are you going to ask a Catholic if she thinks there are no good reasons for believing in the angel Moroni?