Despite appearances to the contrary, science in schools is not just about teaching facts and figures, it is about teaching the way in which humans have arrived at answers to questions ranging from how life reproduces itself to how the stars shine. Science lessons should equip students with critical thinking skills, the most important of which is to ask for evidence for claims about "truth". If we've succeeded in teaching these skills, it's inevitable that some of our religious students will ask "what is the proof for the existence of a god?" and it's inevitable that some of these students will not be happy with the stock religious answers to this question.
One of the things I've always tried to impress upon people on why they should be in a physics class, or learn about physics, isn't that they become experts in a particular area of physics. Rather, it is actually understanding how, and acquiring the skill of how, we arrive at a particular knowledge. The process of inquiry, and how we analyze if something is valid or not, is such an important but undervalued skill. We make decisions based on what we think are valid, yet many people do not realize that what they accept to be valid has not been clearly shown to be valid. In science classes, and especially in physics classes, these analytical sequence of investigation should be taught and shown explicitly, so that students can see how we arrive at a knowledge. It needs to be shown that if it cannot be done this way, then the conclusion that one draws is (i) may be faulty and (ii) not unique, i.e. there could be other conclusions to explain the same thing. The latter is clearly the case where religion is concerned since we have multiple religions in this world all vying to explain the same thing, and all claiming to be the 'truth'.
The greatest contribution to society out of science classes is to produce students that have the skill for analytical thinking. We need not have them become scientists. We only need to give them the ability to think logically and analyze "data" systematically.
Are you a science teacher? Have you been asked the same question?