Why is there a modern misconception about Christianity and Science?

I think a lot of it has to do directly with Darwinian evolutionary commitments around the creation of life on earth and the contrasting commitments of the "young earth" creationist view, and the way the conflict between those two positions became a key way of framing identity for some of the most vocal and visible Christians (and some of the most vocal and visible scientists) over the course of the last century.

In particular, I would look at the books of Richard Dawkins as some of the most influential recent writings that promote the notion that Christianity and science are incompatible.

Personally, however, I think the current estrangement between Christian and scientific belief is a historical anomaly. Even now, I would say the polarization is much less than even twenty years ago, and continuing to lessen.

All truth is compatible with itself.

No religion on this earth has all the answers, neither does science. Otherwise we would be as God, having all knowledge. But as you come closer to pure truth you will realize that it has no distinctions such as science or religion. They are just the means of discovering truth. (They are very good too).

Truth is truth and is not divisible unto itself.

I hope this helps and makes sense, because it is true.

If you want a book about this topic, check out the Dallas Willard book: Knowing Christ Today, especially Chapter 3: How Moral Knowledge Disappeared.

A very short answer is that when science started revealing mistaken assumptions in Christian theology, the Christians of the time ended up ceding the realm of knowledge and drawing a false distinction between knowledge and faith.

For a video answer, I LOVE Ask the Smart Man Q&A between Dallas Willard and John Ortberg. There are bookmarks to topics w/in the two sessions of the Q&A session. Of particular interest are the questions labeled Knowledge and Science and Faith.

For an article by Dallas Willard about Christianity and logic see Jesus The Logician. One quote from it is:

There is in our culture an uneasy relation between Jesus and intelligence, and I have actually heard Christians respond to my statement that Jesus is the most intelligent man who ever lived by saying that it is an oxymoron. Today we automatically position him away from (or even in opposition to) the intellect and intellectual life. Almost no one would consider him to be a thinker, addressing the same issues as, say, Aristotle, Kant, Heidegger or Wittgenstein, and with the same logical method.

His concluding paragraph is:

Paying careful attention to how Jesus made use of logical thinking can strengthen our confidence in Jesus as master of the centers of intellect and creativity, and can encourage us to accept him as master in all of the areas of intellectual life in which we may participate. In those areas we can, then, be his disciples, not disciples of the current movements and glittering personalities who happen to dominate our field in human terms. Proper regard for him can also encourage us to follow his example as teachers in Christian contexts. We can learn from him to use logical reasoning at its best, as he works with us. When we teach what he taught in the manner he taught it, we will see his kind of result in the lives of those to whom we minister.

The essence of any answer to your question must emphasize that the misconception about Christianity and science is very modern. It is modern secularists that desire to rewrite history by making claims that Christianity's job, as it were, is to hinder scientific advancement. For every example they cite, like the church vs. Galileo (his observations proved the earth was not the center of the universe), there are thousands more that prove otherwise. Many of these can be found in secular shows on the History channel. In a recent example about the Dark Ages (sorry can't remember the shows name) they concluded that, without the church keeping reading and writing alive, the Dark Ages could easily have lasted much longer. So any arguments that assert some general obstruction by Christians of scientific advances pre-Darwin are weak. I could go on: the USA exists because of good Christian men; the country's oldest university, Harvard, was founded to train clergy...

After Darwin, it became much easier to inflate the conflict between the Christian and secular worldviews since the secularists could "explain" away life without relying on God. Christians in those times felt just as threatened as those who convicted Galileo of heresay. Look at any modern astronomy text to see this taken to its ultimate absurdity - that the Big Bang started itself. They have to overlook a big contradiction born of the laws of physics (an external force is required to change a system in equilibrium). Fortunately, the archaeological evidence of the past hundred years and the biological evidence since DNA was discovered has disproved macro-evolution (that one species can evolve into another). This has finally begun to turn the tide against evolution but it is still taught in classrooms and promoted by secularists as fact. After the Garden of Eden fiasco, truly evolution has to be Satan's biggest win.

Which brings me to the bottom line answer to the question of "Why?". The problem is not that the secularists are stupid or are ignoring the compatibility of the Bible, Christianity, and science. The problem is that they are blind. The Bible points this out many, many times. Man's soul was corrupted by sin because he wanted to do things his way and not God's way. Until that is fixed, there will always be misconceptions about Christianity by those who oppose it.

Your question is not simple and so my answer is not short. I hope it added something positive to the discussion.