Hi wavydog,
I don't think either side intended it. But I think it was the consequence of, on the one hand, a set of beliefs based on fixed and eternal truths written down in a book, and on the other, an ever-changing set of observations about the book of nature.
Structurally, those two ways of thinking are bound to come into conflict. One is all about permanence. The other is all about change.
The result - when the church was in its pomp - was that scientists were either burned (eg Giordano Bruno) or silenced (eg Galileo).
In the long run, this resulted in a loss of prestige for the church as a source of wisdom. Nowadays, outside the USA, it is fairly rare to find folks who dispute science using the bible as a tool. Religion tends to inhabit a different space: one which science cannot discuss with authority - stuff about morality, virtue, compassion, guilt, afterlife etc. Whereas scientists study nature.
That makes for a peaceful state of affairs. No one needs to call folks who think science is valuable arrogant. Instead, they might see them as contributing to our understanding of the world we inhabit.
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