Yes and no. Totally unused DNA would accumulate changes faster than DNA that was actually used for something (including both genes and non-coding promoter regions), so the greater difference in noncoding regions may just reveal that noncoding regions are mostly junk DNA (and research along other lines indicates that it is).
In order to conclude anything about whether the *significant* differences between human and chimp DNA (i.e., the DNA differences that actually make some kind of *actual* physical or behavioral difference between the species) are more in the genes or more in gene expression, you'd have to first specifically identify the promoter regions and then compare *those* against the coding regions of the genes.
And this is further complicated by the fact that some genes themselves act in the expression of other genes, etc.
I should have been more clear about what I meant. The article refers especially to changes in promoters (non-coding regions of the DNA) and I find that compelling.