A bit late to the game here, but in case anyone else wonders how to do this, it's explained in the ReadMe.txt:
"Each zip file is named by the synset noun offset as an eight-digit zero padded string. For example, bench is contained within 02828884.zip since the WordNet synset offset for bench is 02828884 (you can browse WordNet 3.1 online)."
So, for example the "bottle" synset is "02876657", so changing the zip link above from "shapenet.cs.stanford.edu/shapenet/obj-zip/02828884.zip" to "shapenet.cs.stanford.edu/shapenet/obj-zip/02876657.zip" downloads a zip file including all bottles.