There's a scandal surrounding Blackwater, a private security firm that contracts with the US military in Iraq. I don't need to get into the specifics here, but there's civilian murders, general disregard for Iraqis and their laws, and drunken, post-Christmas-party politician-bodyguard-shooting. (The Blackwater guard in that case didn't face charges, but he did lose his Christmas bonus. His wrist is still smarting.)
So, Blackwater is clearly a nefarious organization. The founder even stole his nameplate on his way out of a Congressional hearing. However, this shouldn't surprise anyone. They're called Blackwater, a name that to me suggests pollution, dark magic, dead bodies in a river, the stuff that the Dave Matthews Band dumps out of their tour bus. How could you not believe an organization called Blackwater was up to dirty deeds?
Charles Dickens would reject "Blackwater" as a character name due to its lack of subtlety. "'Krook', yes. 'McChoakumchild', absolutely. 'Blackwater'? I don't want to insult my readers' intelligence here."
In The Bourne Ultimatum, they at least go with "Blackbriar" as the name of the dirty assassin-training program - at least that evokes nature and life somewhat, not filthy puddles of oil-saturated water. "Blackwater" means kidney disease, explosions of algae, and water that's full of fecal matter, much like Blackwater owner Erik Prince's Congressional testimony.
I would trust a mercenary army called Cobra more than I would one called Blackwater. Say what you will about the tenets of the Cobra Commander's philosophy, but at least it's an ethos.