You don't have to be an Evangelical Christian to be fed up with the way science is taught in the primary and high school classroom these days.
Science is different from Belief. There is a process to science. Some folks propose hypotheses, with which anyone can make predictions (otherwise the hypotheses are useless and mostly ignored). Those predictions are then tested.
Over time, we get some confidence in old theories that haven't been proved false. Confidence comes from checking theories on your own, and it comes from confidence in other people checking theories. We develop confidence in the journals where their papers are published from the occasional well-publicized mistakes. People who cheat are found out, and that news gives you confidence that the system is checking claims being made. Some scientists make great names for themselves, but their theories are still checked and contrary evidence is received with skepticism, but if validated, fanfare.
New science has not yet earned this confidence. For example, string theory is not yet well accepted, but much of quantum mechanics is. It's fun, and the continuous stream of claims and counterclaims is not surprising once you understand that these are younger and untested theories.
Belief, on the other hand, is not about making falsifiable predictions. Belief is about understanding yourself, what you should and should not do. It's about morality and emphathy.
To science, there is no difference between Mendel experimenting on peas and Mengele experimenting on Jews. It's just data (in both cases, unscientifically falsified to try to prove a point). There is a huge moral difference, of course, and that's where Belief comes in.
The trouble I see is that most science education doesn't teach science. Instead, science education teaches something like Belief in scientific theories. The result is neither science nor religion, but a glib materialism that assaults religion and cherishes a lack of critical thinking. I think many conservative religious leaders are right to think that science is being taught as an alternative to religion. Many people, me included, would like to see this kind of teaching banished from the classroom. I'd like to see reporting with the same mindset laughed out of the mainstream media while we're at it.
That doesn't mean I want to see equal time in the classroom for Intelligent Design. I know Intelligent Design is not well accepted. More worrisome, I have heard of no actual hypotheses with which independent labs can make testable predictions. The alternative theory, evolution, has a long productive history, during which many papers have been written and a great deal of elaboration and independent verification has taken place. There is no such productive history in the scientific literature for Intelligent Design, and so I have no confidence in it.
Religious leaders appear foolish when they attempt to construct alternative science, because they appeal to authority rather than verification. Usually this happens when people interpret ancient texts too literally. Genesis says the world was created in 7 days several thousand years ago, and all the animals were created at one time. Unfortunately for literalists, we have a lot of physical evidence that says this planet was created 4.5 billion years ago, and has experienced an evolving population of fauna subject to periodic mass extinctions. I have confidence in much of that evidence and the generally accepted scientific interpretation of it.
On the other hand, Jesus is reported to have said, "do unto others as you would have them do unto you". This shows up in the mathematical literature under game theory, which frankly hasn't given me a whole lot of insight or motivated my compassion for other human beings. But I've always enjoyed listening to sermons on this kind of thing, I love the singing in church, and I often find I have a refreshed appreciation for the condition of others after a good service.
As an aside, I don't really understand this need to interpret texts so literally. The need for continuous discussion and contemplation of morality is not based on the number of days it took for the world to form, either according to physical laws or divine will expressed any other way. The need for morality comes from our being intelligent social creatures living in crowded conditions.
If we are to have a debate about the seperation of Church and State in the classroom, let's have it about what gets taught in Civics. Civics teaches what you ought to do and ought not to do in civil society. It requires us to agree on a common set of beliefs. Since many religious leaders around the world regard the existence of other religions as anything from irritating to blasphemy to a justification of murder, this is clearly an area deserving of robust public debate and continuous refinement.
Meantime, let's see some real science being taught in the science classroom. Kids should be taught to check theories, but they should also be taught to check primary sources in the literature. They should learn about the process, read reasonable-sounding theories that were disproved, and how. This way we can grow their confidence in older and more accepted theories. This way they can learn to listen with skepticism to the endless litany of new claims brought forth by medical researchers testing small groups. This kind of education can help prepare them for the world.