Standard practice for generating rarefaction curves from Next Generation Sequencing data
I actually work in the same group as Chris (QIIME author), so I hope this helps: An explanation he gave to us a while back about the basis of rarefaction curves is just to give an indication of whether your sampling is reaching saturated diversity, when comparing 2 unequal samples.

If you compare 2 samples, where sample x has less information (reads/amplicons etc) supporting it, you can't be sure you've sampled all the possible diversity.

Thus, you plot the number of OTUs you see for increasing numbers of reads. If you're saturating the diversity you should see it plateau.

To bring the 2 samples inline with the 'amount of supporting data' they have, you randomly sample the data of the larger dataset, so that it is equivalent to the smaller, and then compare the number of OTUs each is reporting.