Genetic drift is the change of allele frequencies in a population due to random sampling during reproduction. This can cause some allele combinations to become more or less common than would be expected without drift, thus creating a disequilibrium. However, it's the combination of genetic drift AND selection that generates negative (instead of positive) disequilibria. From the discussion of the article you linked to:
Selection eliminates positive disequilibria more efficiently than it eliminates negative disequilibria, because negative disequilibrium reduces the genetic variance upon which selection acts. Consequently, the average disequilibrium over loci ... becomes negative over time.