I want to write something short about the difference between religious and scientific domains of inquiry.
Sciences aims to expand our knowledge of the world, which I think we all agree is a good and necessary thing. There is however a restriction: this knowledge must be repeatably testable in controlled experiments. This means that there are things slightly outside the reach of science: the existence of unicorns, for example. Although we can say with extremely high probability that unicorns don't exist, science cannot prove that they don't. With unicorns it's easier, since we inhibit the same environment as they do. With beings like God, it's a lot harder to say whether He exists or not.
That's where religion comes in. Besides telling people that God exists and is loving and good, religion also tells us that God wants us to treat others kindly, to respect other people's properties, and so on. As with the existance of God, there is no morality in nature, and thus no truth to find. Religion or philosophy or something similar is needed to give us direction as to how we should act, and what our purpose in life is.
The problem, in my opinion, arises when religion talks about the natural world - claiming that animals did not evolve, for example. There is clear evidence which supports evolution, and science offers the better explanation of these processes than religious texts. Other similar topics include the possibility of a world wide flood, dividing the Red Sea, and so on. Just as science cannot offer much in terms of morality, religion is lacking in its explanation of natural phenomenon.
This shows that religion and science actually have mutually exclusive domains, and hence my problem (if I have one; I'm still deciding) with religion does not come from science, but from something else.