Regarding the points that article makes about Antony Flew, I recommend you also read
this article by Richard Carrier regarding Antony Flew’s “conversion.”
The article argues that teaching intelligent design would not violate the separation of church and state. I would recommend reading the text of
Kitzmiller v. Dover, in particular section E, which applies the Lemon test - the accepted test for separation - to this issue in detail.
The article then equates deism with pantheism - which is a bad idea - and then argues that Einstein’s science is actually based on pantheism. Einstein might have been a pantheist, but even if he wrote his theories because he thought little blue fairies told him to, that wouldn’t matter. Eintein’s theories have been verified by the scientific method (whatever that is), not by pantheism. One can believe in relativity and think pantheism is just silly.
Then the article claims something along these lines: supporters of evolution claim that intelligent design is not science, because it is not materialistic. Regardless of whether or not they claim this - regardless of whether or not intelligent design reallly iis science or not - it is bad science. It is not supported by the evidence.
The article then attempts to show that evolutionists do not have integrity. Whether or not this is true has little bearing on whether or not intelligent design is good science. One point that I would, however, like to address in particular is this one: “Evolutionists claim if ID were good science, we would see more pro-ID papers published in reputable journals. But these papers have an anit-ID bias that leads them to immediately reject ID papers.” This claim would be much more plausible if the author compared the percentage of pro-ID papers that get rejected to the normal rejection rate - but I have yet to see a list of rejected papers.
The article makes the claim that many biologists don’t know what the Cambrian explosion is… which I find mildly implausible. That aside, the article also acts as if the Cambrian explosion lasted a week or so. The most reasonable estimates put its duration at five to ten million years, with some closer to forty.
TalkOrigins as usual has a nice discussion of the Cambrian explosion re intelligent design.
The article also makes the “information argument,” which is mildly implausible. I don’t want to go into details, but it seems that if this were true, genetic algorithms could not work - and yet they do.
It argues that punctuated equilibrium points towards an intelligent designer. Again, the article seems to misunderstand time scales. Gould’s rapid periods of change could last over ten thousand generations.
For more information regarding these bad arguments, either wait for one of the people in this forum more concerned with evolution to show up, or go look at TalkOrigins, which is very, very comprehensive.