Digital Genomic Footprinting for ENCODE
After reading the paper cited I think the logic goes like this: DNAse I will create free ends at accessible sites in the genome. However shearing during subsequent DNA isolation is also a source of free ends, and these represent noise in the analysis. You have to put in a lot of energy to shear DNA to very small fragments, so I infer that mild shearing during DNA isolation is very unlikely to create a new end that is near to an existing DNase I-generated end. Therefore, under the conditions used, any small fragments are much more likely to have been generated by two closely-spaced DNase I hits. By limiting the analysis to these fragments the noise from shearing is minimised.

Now that I've written this answer it doesn't seem like much more than a rewrite of the emboldened sentence, but I hope it is helpful anyway.