I think that one of the problems many people have with the attempt to explain the world using science is the issue of reductionism. Many see reductionism as an attempt to take all of the emotion, beauty, and mystery out of the world, and replace it by cold, mechanical, and simplistic scientific explanations.
To answer this, I would like to draw a distinction between useful or good reductionism, and useless or bad reductionism. For the scientific endeavour, reductionism is essential, as the natural world is far too complex for us to fathom otherwise. We need to attempt to reduce complex systems of interactions to simpler or more fundamental things, create hypotheses based upon these simpler explanations, deduce and test the predictions of these hypotheses etc. Without reductionism, science would be too difficult for us to do. So, where reduction allows us to make progress in the scientific endeavour, I would classify it as good reductionism.
By contrast, we might try to understand the causes of Islamic extremism by reducing everything to the interactions of fundamental particles. This would clearly be a hopeless task, and would be highly counter-productive. Whilst I think that all macro phenomena probably can be reduced to the micro (notwithstanding the mooted issues with emergentism ), there are many cases when this makes no sense at all, as it adds nothing to our understanding, and makes the task more difficult instead of less. When analyzing some aspects of the world, such as the societal, religious, and ideological drivers that lead to extremism, we do much better to stick to macro explanations.
So, we have different levels of explanation that are appropriate in different circumstances. Having said that, I think that we are often not in an either/or situation with regard to reductionism. For example, when looking at the human emotion of love, I think that the reductionist approach (by looking at evolutionary and biological aspects of human emotion), and the non-reductionist approach (experiencing love, reading romantic novels, poems, sonnets etc.), actually complement each other. That is, I think that the greatest understanding of love comes from looking at all the useful levels of explanation, and not just concentrating on one. Generalizing this, I think that we need to know when reductionism is useful in understanding the world, and when it is not, and seek enlightenment accordingly.