So here's the simple justification for this atrocious behavior in public schools: it's based on the scientific method.
Before you go off on how flawed evolution is, how imperfect our knowledge is, how much controversy there is in the scientific community concerning available evidence, let me repeat the above: it's based on the scientific method. This means (as a pastor kindly pointed out, when I was last in church) that scientists change their mind, and expect to do so. Most will gladly tell you that they don't have all the facts, and even when they do, that's still no guarantee that theories they provide are necessarily in line with "what actually happened."
A theory is invalidated when counter-evidence is found. It loses favor when another, simpler, theory is offered. This second part has an "artistic" side to it: you might assume it's simpler to believe that your state's department of transportation is responsible for fixing the roads rather than, say, a horde of goblins, but a lot of people also think it's simpler (more elegant) to believe a god of some form created the universe for the purpose of having human life rather than the process(es) of evolution, natural selection, etc. Picking a "pretty" answer from a set of theories which could all equally-well explain a set of facts is difficult work, and from what I've said above, there's no right answer.
There's a third part to this: a theory's value is measured in terms of predictive power. Not only should a theory be able to say "things are the way they are because ..." but it should also be able to say "... and things will, in the future, most likely be as the following ..." We don't have theories for the purpose of explaining what has already happened. Although this is of great interest to a great many people, the real value of theories is in predicting the future and, as a tool, helping us make decisions. Based on available evidence, I might conclude that the movement of planets is based on someone's whim. While this explains the facts (gives them a "reason" which you can't prove to be a lie) it does not help me predict where planets will be in the future. But assume for a moment that the above were true, that planets really do move based solely on the whim of some random person. What happens if I come up with a theory which describes planetary motion such that I can predict future positions and always be right? Although my theory is wrong (as stated above, a person's whim is the deciding factor), we have a useful tool for the future, one which, so far, has proven itself reliable. Theories are, therefore, tools, not history books.
Why, then, are various forms of evolution taught in public schools? We don't know that evolution, as presented, is "absolutely true". In fact, not everyone agrees that what's taught is necessarily the most accurate representation of what even a subset of scientists believe to be a good theory. Given the same facts, different people come to different conclusions. It's part of the process. Over time, new facts are dug up and new theories drawn up to match available facts. Occasionally, a fact is challenged on the basis that it does not match currently accepted theory: this isn't a bad thing; if a detective is going through evidence for a case and finds an "outlier" which doesn't match what he's currently expecting to find, he's going to want to re-check the evidence as well as his expectations, as one or both might be wrong. Haven't we even heard of court cases where someone was found guilty, sentenced, and occasionally even executed, only to later find some missing piece of exhonerating evidence?
Being wrong happens. What counts is having a reliable method of finding out the truth, or at least something close enough to the truth to serve as a day-to-day tool. The scientific method is very much that tool for us: it allows us to gather facts, attempt an explanation, verify that our explanation matches all current evidence, then iteratively refine our idea until no more problems are found. So long as a theory is useful and sufficient counter-evidence has not been found to completely invalidate it, it is kept, used, and taught.
You won't find a lot of pastors preaching the evils of the theories of gravitation or relativity. Quantum mechanics, though only a theory, are taught in schools without a peep from the pulpit. Evolution, and in general theories of origins, are the only ones routinely attacked, sometimes on scientific grounds, but most often on emotional or political ones.
Newton's theories are still taught, even though they are now known to be only approximations of the more accurate Einsteinian theories: like household measures, his theories of motion are "good enough" for most common cases, but they do not fit observable facts over the whole range of observed situations. Again: his "laws" are still taught even though they are known to be "false" in a certain sense. Should we not hear an outcry over this? Is this not terrible?
I often hear that evolution has not been proven true. It cannot be: the scientific method is only useful for proving something false, not true. I hear arguments by consequence: children taught these theories no longer value human life, because it is (so the complaint continues) just the result of random selection; children no longer say "wow" to the world. Aside from the logical fallacy, there's also this: if life is really as unlikely as intelligent-design proponents claim, should the odds themselves not cause us pause? Should we not value human life, and all life, at least on the basis that it is the result of a process which selects the local-maximum (not-quite-perfect-but-stil-better-than-others) solution? I hear complaints that, because of standardized testing, children will be forced to believe these false theories. Can children not pass the test while believing the answers they're providing to be false, or at least (as they should) merely theories? I don't know about you, but I've always found it's easier to pass a test if you know what it is the teacher wants to hear. Children are smart enough to do both things: believe whatever their parents tell them and remember what their teacher taught them to recite.
It is honest for the government to pay public schools to teach some form of evolution. Based on current scientific evidence and continuing research, this is the most accurate theory we can provide to children which is still based on the scientific method. It does not explain things as well as "because God said so", and honestly, theories of origins don't have much predictive power on which to judge them. Religious ones might eventually be testable, but not under controlled circumstances, and not at the whim of a researcher. So long as the government is providing to children whatever the latest, most accepted, least challenged scientific research happens to be, it is following the safest course of action. The source of the information is accountable; theories are made to fit the facts, not the other way around; there is honest adversarial dialogue to try to hit the nail on the head.
I encourage you to teach your kids whatever you like. I encourage you to challenge the theory of evolution based on observable facts, out in the open, above-table, honestly. There's plenty of evidence out there you can use against existing theories of evolution, if you care to contribute. If we can find a theory which more accurately fits the evidence, is testable, is useful in predicting the future, and can otherwise benefit us as a whole, great. What I don't recommend is asking schools not to teach evolution because it's not "proven to be true" -- we might as well not teach the theory of gravitation, either. I also don't recommend asking schools to teach the biblical Genesis story as "equally valid" theory. Doing so is just inviting members of every other religious faith (and a few quacks who think they're funny) to also beg/pressure schools to teach their personal favorite theories too -- do you want your kid going to school to hear about how a pair of birds created the earth by reaching down and pulling up some dirt from the bottom of the sea? Maybe that'd be fine in a literature, culture, or other such class, but it's not fine for a science class.
(Incidentally, the same applies to a lot of prayer-in-school requests, where parents fail to realize that getting their proposal passed opens to the door to people of all faiths asking for equal treatment: do you really want your muslim neighbors convincing the school to have three or so prayers per day at scheduled intervals? You want to wear a cross around your neck, but you're offended when someone gets to wear a satanic symbol? That reminds me: the satanic bible is really just a secular-humanist handbook, a sort of dog-eat-dog view of the world. There's no real devil-worship in there, though it's just as evil from certain points of view.)
If you're worried about synchronizing your religious views with available scientific theories, you can do as some churches have done: adopt some science into your religion. Some pastors preach that God simply made things look old in order to fool us (or make us go "wow"), which is why scientists find "faked" evidence. Some preach that the bible is only allegory for simple people, because the story matters more than the facts. Some have been convinced by evidence to the point of preaching punctuated evolution: everything is as described by scientists, but every now and then God decides to have some fun with things, to gently direct an otherwise agnostic system toward his desired goal. Others teach a God of the gaps; wherever randomness is found, insert God. Einsteinian physics are rather deterministic, and not very comfortable in terms of "free will". Luckily, we can't predict the future by observation (Heisenberg's uncertainty principle shows this to be true) and with quantum physics, we have randomness back (randomness which, happily, acts in a generally-predictable way for household use.) God therefore gets inserted into quantum physics, and for those with such tastes, into string theory. Sometimes people are more concerned with being comfortable than being right. Do what seems best to you.
Evolution, therefore, is taught not as fact, but as theory. It is taught because it is the result of a process which seems reliable, if iterative. There is no end to the scientific method; theories are never simply proven true, there are always ready to be challenged. This method sets theories apart from any other available ideas about origins (or anything else), and is a fundamental difference between teaching biblical Genesis and teaching some form of evolution.
