So a dictionary defines chilling effects as the inhibition or discouragement of the exercise of your rights.
Let me frame the thought by giving an example: if I am talking with someone, I might not say a few things because, hey, the TLA might care enough to pull the record and listen in. Or we take care to communicate with GPG or something. It inhibits what we do. We can still vote; our vote actually has meaning; our votes actually change the elected officials, etc. We still can run a socialist candidate (c.f. Kshama Sawant 2013 in Seattle) and they aren't shut down via police action or other hardcore discrimination.
This is in contrast against what it could do: it could be always used to harass and discriminate against those dissenting from the Two Parties and the State. Anyone who said anything would be looked at and actions taken to shut them up and limit the expression and formation of dissent.
While the database of communication could be used against people to significantly disrupt everyone who speaks out, it is not, and in my opinion, it will take a few emergencies like 9/11 to actually alter the mindset of the US to make that acceptable. Of course, people are harassed; some people are okay with that. It doesn't mean there's general acceptance of that, and it doesn't mean everyone is harassed.
Thus I draw the distinction: people self-censoring vs. the heavy hand of an apparatchik forcing change. The first is very immediate and to-hand; it's reality today. The other is possible, possibly even probable given certain courses of events, but fear-mongering is not the best way to go; let's deal with the clear and present threat at hand- chilling of free speech, chilling of dissent, chilling of the business interests of United States citizens, (frankly, these all apply outside the US as well, and hopefully the debate within the US around privacy and data capture also places the operations of TLAs on non-US citizens & non-US soil within the public purview of the United States citizenry via their elected representatives).
Fear does work as a campaign tactic, but the reality is, fear is not something people want to work for. People are willing to work for hope (didn't we all see that in 2008?), and I really would prefer the pro-privacy, pro-4th amendment activists focus on the positives and hope of what we can do rather than performing the traditional stick of the Republicans & Democrats (vote the other way and the free work and the US will END!!!11!oneoneone). It is in hope of being not being tracked against my will, not being monitored in every phone conversation, not being advertised at without my consent that I advocate for these changes to come to pass. It is in hope that I can say thoughts and perform actions online and offline and feel the liberty of not having peeping government Toms and raucous advertisers know anything about me.
So there's my distinction and my spiel. :-)