You make good points, Werecow. But none of them were made by Prothero. Instead, he went straight to impugning Plimer's motives, accusing him of being corrupted by his association with mining. That is a nasty thing to say about anyone, let along a University professor, and was clearly designed to persuade people not to even listen to him.
Others already made this point, but if you consider it morally outrageous that Prothero accuses Plimer of being intellectually dishonest, why can the same not be said about Prothero's depiction of creationists? He accused Gish of lying, after all - he explicitly states that he thinks people like Gish know that they're not telling the truth. That has to be up there with pointing out that Plimer's a mining geologist.
As for pointing out Plimer's potential conflict of interest, well, call me crazy, but I don't think it's a huge coincidence that the American Association of Petroleum Geologists was the last scientific body of standing to drop the skeptical position on climate change as their official stance. Given how far Plimer deviates from the consensus position on nearly every point, it's hard to imagine that the dissonance caused by his occupation hasn't influenced his position on the matter.
Now, to be fair, Prothero isn't a climate scientist either (although he has done research on palaeo environments and their impact on the ecology of the day), but he's just relaying the position of a large majority of scientists in that field, whereas Plimer slams head first into that consensus.
If you're interested, there are many more points of contention in
this point-by-point critique of Plimer's Heaven and Earth by Ian Enting (warning, it's 46 pages long). Or there are various shorter rebuttals out there. One bit from Tim Lambert's
book review stood out for me. In his book (which I confess I have not read), Plimer apparently cites a paper by two petroleum engineers, Khilyuk and Chilingar. This study is rather infamous among people interested in climate change. What did this study do? Here's an excerpt:
Recalculating this amount into the total anthropogenic carbon dioxide emission in grams of CO2, one obtains the estimate 1.003×1018 g, which constitutes less than 0.00022% of the total CO2 amount naturally degassed from the mantle during geologic history. Comparing these figures, one can conclude that anthropogenic carbon dioxide emission is negligible (indistinguishable) in any energy-matter transformation processes changing the Earth's climate.
(emphasis mine)
They compare the anthropogenic emissions of CO2 released over 200 years to the
total amount of natural CO2 degassed over geologic history and conclude that we can't possibly be significant. Yikes. That's not just a little wrong, it's a lot wrong (more on that paper
here). Apparently, Plimer cites this paper not just once, but three times. And from what I've read, there seems to be a lot more cherry picking of flawed papers going on than merely that one example.
And the thing to note is that Plimer is presented as an expert to the unsuspecting public. If he was a backwater geologist with some controversial ideas, Prothero would probably not have picked him to criticize. But by contrast, Plimer may well be described as global warming skepticism's nr. 1 Australian spokesman. In doing so, he sells absolute pseudoscientific nonsense to his public, and it's not wrong to point that out.