Sub-sampling is not admissible?

Hi all,
I was reading a recent paper by McMurdie & Holmes called “Waste Not, Want Not: Why Rarefying Microbiome Data Is
Inadmissible” (PLOS Computational Biology, 10:4 - e1003531), where the authors state that “…rarefied counts result in a high rate of false positives in tests for species that are differentially abundant across sample classes. Regarding microbiome sample-wise clustering, we also show that the rarefying procedure often discards samples that can be accurately clustered by alternative methods.”
I’d be very interested to know your opinions on this matter!