The irony of Milloy having a column (and book) about Junk Science is that Milloy is a shill, and presents science within an ideological framework. So "junk" science becomes science where he doesn't like the answer.
The larger problem of not trusting studies is related. If ideology has already dictated what the results have to be, you can't trust it. Sadly, this has infiltrated government-sponsored work, which is supposed to be free from such interference. It has become increasingly perverted by politics in what conclusions are allowed to be drawn, and especially so in the recent past. You get decisions like not approving (or delaying) medical treatments or not dispensing medical advice (or dispensing wrong information) because of political and ideological stances; IOW you'd rather kill people than help them, because you disapprove of their ideals or behavior, or because helping business is worth a few lives. Recent legislation has turned the system backwards with regard to burden-of-proof, or requiring kinds of proof/evidence that science cannot provide.
I'm in the middle of reading "The Republican War on Science" by Chris Mooney. It's good, but scary.