Ah, those were great fun! :-) I wasn't able to attend, but I followed the correspondence and the articles quite avidly.
If you assume that material reality is all there is, then you are only going to look for material explanations, and any explanations that are not material will be rejected out of hand. Fish’s objection is not so much that this is dogmatism but that it is dogmatism that refuses to recognize itself as such.
This is actually a strawman, since it is presuming that atheists "assume" that material reality is all there is, when actually, they don't necessarily make that as an assumption. They might conclude such--and at the same time view all new information openly. Just because geologists believed in Continental Drift doesn't mean they absolutely rejected Plate Tectonic theory when it came out.
Also, note that there's nothing wrong with looking for a material explanation prior to a miraculous one. I think that the germ theory of disease is far better than the evil spirit one, and believing it doesn't mean that the germ theory is "assumed" without evidence.
I have great respect for Mr. D'Souza, but I think he falls way short on this column. I would, however, like to see a discussion between him and Dr. Fish.
Just because geologists believed in Continental Drift doesn't mean they absolutely rejected Plate Tectonic theory when it came out.
Interestingly plate tectonics were swiftly accepted. I doubt atheists think thoughts are material things.