The crux of the article regards the multiple forms of conflict which occur under the umbrella of "The War in Afghanistan"--war between ethnic factions, war with al Qaeda, war with the various groups which are often lumped under the category of "Taliban", and war against narcotics lords.
In short, it's complex. This is one of the central points of one of the best books about counterinsurgency written in the past few years--David Kilcullen's "The Accidental Guerrilla: Fighting Small Wars in the Midst of a Big One".
We use the term "hybrid war" a lot in the milblog community, but we usually use it in the same sense as Secretary of Defense Robert Gates does--to describe a tactical phenomenon which combines conventional and unconventional warfare.
Kilcullen defines "hybrid war" as a framework for understanding the complex environments in which we find ourselves in these days. We're not simply fighting one war in Iraq or in Afghanistan. We're fighting multiple enemies, who take multiple forms: insurgents, terrorists, militias, criminal organizations, and tribal blood feuds.
Take a look at the article, as it's a good description of the complexities of waging war in Afghanistan. General McChrystal is certainly a great general, but I don't envy his job in the least.