One of the most common arguments against intelligent design seems to me to confuse motivation with theoretical basis. In defense of the charge that ID is religious creationism, many opponents of ID point out that most people who support ID believe in a creator God for religious reasons. This happens to be true. Actually, they usually say that all who support ID believe in a creator God for religious reasons, and that's false. Antony Flew supports cosmological ID, and he isn't religious at all. There's a whole blog of ID proponents who are not advocating theism (I believe it's Telic Thoughts, but I couldn't find their statement on this if so). But it is true that most ID supporters are religious theists of some sort.
Here is the important distinction that those who give this argument cannot, or in some cases simply refuse to, see. Members of the Discovery Institute offer arguments for the existence of God. These are classic philosophical arguments that go back at least as far as Plato, who had no contact with Christian (Christianity didn't exist) or Jewish (no Jews were anywhere near him) monotheism. These arguments conclude that it seems likely that there must have been some designer for whatever particular phenomenon the argument is concerned with, e.g. the origin of the cell, the origin of some particular organ, the cosmological constants of the universe, etc. The Discovery Institute also happens to believe the designer that the argument's conclusion speaks of is the Christian God. They even admit that they have religious motives for wanting people to accept the argument. But the fallacy anti-ID people regularly engage in is to take that motivation to be the basis of the argument. It's simply not, and that kind of confusion would lead an introductory philosophy student to fail a critical thinking assignment.
The argument is based on some empirically observable fact, taken together with a philosophical view about what that fact should lead us to conclude rationally and without religious presuppositions. The conclusion is that there was some sort of designer. The empirically observable fact is, as far as I can tell (though I'm not in a great position to judge this), indisputable and a result of our best science. That philosophical view is, as far as I can tell (and I am in a good position to judge this), controversial but well within the mainstream of contemporary analytic philosophy. Philosophers as good as Peter van Inwagen, Richard Swinburne, Alvin Plantinga, Roger White, and at one point Neil Manson were endorsing at least parts of this argument, and now former atheist and current deist Antony Flew has come on board.
When someone happens to believe in God for other reasons and thus is further motivated to want others to see how convincing this argument is, that detracts exactly zero from the value of the argument. The argument stands or falls completely independently from the motivation someone is using to promote it. The objection to ID as religious creationism just confuses the theoretical basis of an argument with someone's motivation for wanting someone to accept the argument. Those are very different things. The fact that many people who try to use these arguments to persuade are doing so for religious reasons has no bearing whatsoever on whether the argument is religious creationism. Many people have had political motivations for supporting minority rights of various sorts, but that doesn't mean the arguments for why we should allow everyone a vote regardless of race are merely partisan arguments. It just means some of the people who voted for this were doing it just to retain power in Congress. Someone's motivations for supporting something are simply irrelevant to how we should describe the argument itself.
Even if the same people who came up with the argument are the ones who are promoting it for political reasons, it is the argument itself that must be evaluated and not the motivations of those who are supporting it. Anything else is basically anti-intellectualism and the denial of the need to evaluate positions and arguments reasonably and fairly. The anti-ID movement is, as far as I can tell, spearheading a new movement to forget about reason and simply dismiss positions out of dislike for them. That kind of anti-intellectualism should not be tolerated, and it's shameful that scientists and philosophers have gotten on board with the kind of irrationality that this objection to ID assumes.
Case in point: Wikipedia's Intelligent Design entry. Unconscionably, they rely on exactly this sort of fallacy in their justification for continually lumping ID together with religious creationism. Take a look at the archives on the discussion page. There's a whole behind-the-scenes discussion between the powers-that-be and those who have tried to have a viewpoint-neutral, indeed an accurate, description of ID. The flow of that conversation reveals that they are immune to argument. No amount of reason or distinction-making is going to change their fundamental and unargued presupposition that ID is religious creationism, and it's a shame that Wikipedia tolerates such nonsense. The only support given for this intellectually dishonest practice is that many of the leaders in the ID movement have religious motives, which as I've just explained is completely irrelevant to whether ID is religious creationism. I tried to make this distinction to see how they would respond, and they deleted my comment and said not to edit discussion archives whose discussion has ended. The key was that the discussion was ended. Their mind is made up, and no amount of reason could ever convince them. That's anti-intellectualism, and it strikes me as a deep irony that anti-ID folk seem to want to portray ID supporters as anti-intellectual while displaying anti-intellectual behavior in order to make that point.
I say all this as someone who is not at all convinced that the biological forms of ID are very good arguments. I happen to think the cosmological fine-tuning ID argument is better, but I can see how someone would resist it. It has some assumptions that I think are plausible to hold but also might be plausibly denied (as long as they're not being denied in order to resist the conclusion, which would be question-begging). I really don't have much desire to push any form of ID, just to make sure it's presented fairly and accurately. But the people who oppose ID have so willingly given up any sense of careful thinking that it just seems to me that they are the clear losers in this fight, at least on the intellectual level. I wonder if the reason this view that they think is so implausible has become so popular is that those who are initially attracted to it have seen that those who oppose it aren't saying anything that touches it. If the opponents of ID would give fair presentations of the issues and then point out where they disagree with the assumptions of the arguments, perhaps many ID supporters would see that some of their premises or inferences are more difficult to support. As it stands, very little that the anti-ID movement says is worth listening to, because the good is drowned out by the misrepresentation of the ID position and the subject-changing tactic of bringing up irrelevant information to distract from the real argument.