Talkorigins is not noted for their dispassionate promotion of science, rather more for skewing and misstating things so that science appears to support atheism.
As for answering some of the points in there, here goes:
The naturalism that science adopts is methodological naturalism. It does not assume that nature is all there is; it merely notes that nature is the only objective standard we have.
Here is one example that clearly shows their presupposition. I guess on one level it is true in that every person observes the same data, however, what is implied here is that the data, according to methodological naturalism, has to be ascribed to natural causes alone. As Christians we do not disagree as far as secondary causes go, but then the following qualifier, nature as "the only objective standard", shows that they consider nature to be the primary cause. That is a serious leap of faith, because for that be true, the observable universe (nature) would have had to cause itself.
Hypotheses that can be asserted but never supported are not part of science.
Who or what decides what support constitutes? Is quantum physics science or not? Cosmology? archaeology? The stock answer here is that anything that can be subjected to the scientific method and methodological naturalism is scientific. That raises more questions than answers though. Basically any human undertaking can be described using the scientific method (
Christian Skepticism - a reasonable faith...: I'm a Golfologist. Not only that, both of those assumptions are philosophical in nature, and cannot be proven by their own assumptions, i.e. prove the scientific method by using the scientific method, or show how methodological naturalism has been "reliably observed" in nature.
#3 is a blind assertion that does not distinguish between primary and secondary causes. It can only be stated that way if naturalism is dictated a-priori. It is also a straw-man argument brought up many times by atheists, as it assumes that Christians believe all things are supernaturally caused. It exhibits no knowledge of the regularity of natural laws that God instituted from creation forward. They may then argue that God serves no purpose in describing these things, but that fails to account for those aspects they hold by faith, such as the reliability of their observations, the expectation of regularity in nature, the reason that the universe behaves in a regulated and consistent fashion etc.
Intelligent design implies philosophical naturalism.
Pot calling kettle?
I hope that helps. There is plenty more to repsond to there, but those were the main points I would address.