For those of you who would like to understand how N2 is removed from the atmosphere (it does, in fact, interact - but does so through biology not merely chemistry), and how nitrites, nitrates, and ammonia and ammonium (products of atmospheric nitrogen) are returned to the atmosphere, perhaps a picture will help. Do you really expect people to say "nitrogen, nitrites, nitrates, ammonia, and ammonium" everyime they discuss nitrogen flow in the cycle?
Is it more clear now? The article is correct. It is accurate science. As an ecologist (MSc, PhD candidate), I agree with the reasoning and causation presented. Until we begin to treat our farms as ecologies, and not factories, we are screwed (note my name).
ps. Human fixation of nitrogen into ammonium and nitrates for fertilizer is usualy over-applied, resulting is most of it "running off" (because of rain) into local fresh water systems and "evaporating" (via bacteria) quickly back into the atmosphere. Carefuly applied fertilizer (timed to growth spurts in plants, avoiding rain, and application directly to plant base/roots) can be far less deliterious, but (as the article mentions) the use of fertilizer is not regulated like the release of nitrogen through combustion. Organic farming, of course, does not use synthetic fertilizers - so it avoids the problem alltogether. The negative results of hapless synthetic fertilizer use go far beyond a mere increase in atmospheric nitrogen, for instance: algal blooms (red tides), destruction of coral reefs (through cultural eutrophication [anthropogenic over nutrient-ation], and "dead zones" at river outlets (see: Mississippi, for example). There is some debate on the extent that phosphorous (from synthetic fertilizers) contributes to these processes. In some cases (the Florida Bay, for example), phosphorous is likely the primary culprit of algal blooms. Sweden has, though world-leading policy and implimentation of fertilizer regulations, largely eliminated excess nitrogen from many lakes, but phosphorous remains an almost impossible problem for them to correct because of its physical and chemical properties (too complex to explain in an already long post).
EDIT: Regarding scientists being "in it for the money", I can tell you firsthand: not ecologists (we don't get patents). Maybe those medicene or genetic engineering guys, but not us farmer/forest/marine (variations of ecology) guys.