A common set of arguments against intelligent design theory is that it, the Discovery Institute, or the motives behind the theory are religious in nature. It is supposed that for this reason, intelligent design theory is not scientific or is not a viable theory. I have previously shown that intelligent design theory is a historical rather than scientific theory. The study of history is distinct from both science and religion. Bearing in mind this clarification, these kinds of objections can be divided into three groups: the fallacy of poisoning the well, the failure to distinguish philosophical argument from historical theory and the failure to distinguish philosophical claims from scientific ones. Since none of groups are sound arguments, these objections against intelligent design theory are all failures.
The first set of objections are based on the fallacy of poisoning the well. This fallacy begins by pointing out the connections between religious belief and intelligent design theorists. The founders of intelligent design theory and the primary organization promoting intelligent design theory (the Discovery Institute) are all connected to religious belief in a variety of ways. Most are Christians or believe that intelligent design lends support to the existence of God. In addition to this, many of these people have promoted Christian moral values, distinctly Christian teachings or even political action. This fallacy completes by claiming that these facts mean that intelligent design theory is either not scientific, not viable or is brought into some kind of doubt. The first set of facts are simply not relevant to intelligent design theory. Kepler believed that his study of planetary motion showed hidden patterns placed there by God. That is of no relevance to the truth of the laws of planetary motion. Similarly, Isaac Newton wrote commentaries on the Bible and believed that he had uncovered the truth buried by ancient conspiracy. But that is also of no relevance to Newtonian mechanics.
The second set of objections confuse historical theory and philosophical claim. The theory of intelligent design is a historical theory. It claims that there is a method irreducible complexity or specified complexity that can determine that some features of the natural world had an intelligent cause. To go any further than that is a philosophical claim. So claims that this cause is divine, guesses as to the purposes of this cause, arguments that this cause designed poorly or was evil are all philosophical claims. All that this historical theory can tell us (if it works) is that there was an intelligent cause. Even if two features both had an intelligent cause, this theory cannot claim that the cause of one feature is the same as the cause of the other feature. In addition to this, intelligent design theory can have plenty of false negatives (by failing to recognize an intelligent cause masquerading as an unintelligent cause). So any argument against intelligent design that relies on the nature, purposes or actions of the designer is attacking a philosophical theory rather than intelligent design. Similarly, any theory attempting to show, prove or support the existence of a designer of any kind is a philosophical theory based off of intelligent design theory.
The third set of objections confuse philosophical claims with scientific ones. This is complicated, especially because a numbers of scientists are deluded enough to believe themselves competent to answer philosophical questions. Intelligent design theorists sometimes claim that any study of causes should permit there to be supernatural causes. They may also claim that intelligent causes can not be ruled out since we already use them in various historical disciplines. These are two separate claims. Since these claims are made in a context that ignores distinctions between science and history, there is no simple answer to them. On the other side, many scientists claim that methodological naturalism rules out supernatural explanations. They also claim that without supernatural explanations, intelligent design offers no theory. Once again, this groups fails to properly distinguish these two different claims or to distinguish between history and science. Nonetheless, the difference between science and history, understanding what good science and good history are, whether or not supernatural or intelligent causes can be permitted as explanations and what place methodological naturalism has are all philosophical issues. None of them are scientific issues. So science has little to say in these kind of discussions either for or against intelligent design theorists.
Any connection between religion and intelligent design theory is simply a distraction from the real issues. The real issue is whether or not the claims of intelligent design theorists are true or false. The real issue is whether or not intelligent design theorists can actually detect design or not. Religion has nothing at all to do with these claims, so it functions as a bogeyman so that the real issues can be avoided.