How do you know the other guy with the same collection you have is a terrorist or an enthusiast? You don't just by the fact that he has several guns so you must determine if there are other indicators before assuming it equals terrorist activity. That's what the DHS bulletin is warning LE to not make the mistake of assuming. That's the crux of the matter.
The problem is, Law Enforcement are just people too. (Well, some of them)
If 80% (just throwing a number out there) of gun owners think this means "people who have lots of guns and ammo, might be a terrorist", they it stands to reason that a lot of (being human) Law Enforcement Officers might come to the same conclusion.
Social thought engineering takes time, patience, and a skillful hand to deliver messages which subtly shift the public perception over time. Bulletins like this are a perfect medium for this because they are circulated through official channels and delivered to an audience which is responsible for enforcing the government's authority.
"Hey, that guy has enough firepower to rival our police agency. But he's OK because we know him and he's lived here his whole life."
Slowly evolves in to...
"Hey, that guy has enough firepower to rival our police agency. Sure, he's lived here his whole life, and we know him, but really.. what is he planning? Why does he need all of those guns, all of that ammo?"
This is nothing more than an extension of the powers that be continuing their anti-gun social engineering. It wasn't 2 minutes after Aurora and Newtown that the anti-gunners were on every medium available screaming "PEOPLE CAN ORDER THOUSANDS OF ROUNDS OF AMMUNITION OVER THE INTERWEBZ!"
And not long after, a ban on private purchase of ammunition in NY happened, restrictions and reporting on quantity, etc.
This tells the general population - via their authority role models - that "owning a lot of guns and ammo is wrong. Good people don't need to do that. Sportsman don't need to do that. Hunters don't need to do that. Only people who aren't quite right in the head do these sorts of things."
Not being paranoid, or reading more in to it than I should; just watching it unfold, with some understanding of what the pieces (like this bulletin) mean in the overall game plan.
I've studied Dr. Josef Goebbels and read his diaries. Not especially fond of socialism, but the old Doctor from WWII was incredibly adept at bending public will to the favor of the party. I can see the same tactics being used today to get people to accept National Power, and believe that The Government Can Do No Wrong.
Sometimes propaganda is a big stick. Sometimes a small stick. Sometimes you don't even know you've been handed a stick to carry.