I assume they're collecting everything, but I'm not quite sure if I'm ready to buy that they're analyzing everything (beyond maybe a cursory inspection to classify traffic type very generally).
People are worried about the NSA because it was the NSA that was found to be responsible for the Room 641a scandal (http://en.wikipedia.org/wiki/Room_641A) in which it was discovered that they were tapping massive amounts of domestic internet traffic without a warrant or probable cause. There are probably another 10 to 20 more of those rooms strategically placed around the country, all of which would be indiscriminately tapping domestic internet traffic (http://www.wired.com/threatlevel/2012/03/ff_nsadatacenter/al...). Additionally, the NSA employs more people than the FBI and CIA combined. If there's any agency tapping your internet usage it's the NSA.
At the moment they would be able to do that, but there are bills constantly being introduced (and so far, luckily, shot down) to Congress calling for mandatory data retention. The current bill calling for this is HR 1981:Protecting Children From Internet Pornographers Act of 2011 (http://www.govtrack.us/congress/bills/112/hr1981), introduced by Rep Lamar Smith of SOPA acclaim.
For a brief moment after reading that I had to consider if the article was satire.