I guess how much of a risk this depends on where you see the vector of attack. If you think the NSA has one decade forward on decryption ability, then what does it matter if Facebook/etc hands over the data or if you've trusted another encryption scheme?
But consider this scenario: the NSA knows that one member of a group may be a person of interest, with the rest being innocent (for example, a leaker within an organization). What draws more attention: the person who is sending all of their traffic through GMail, etc...or the person who, for some reason, is using an obscure service at particular hours of the day? Even the use of Tor might be a flag.
And if your counter-argument is, "Well, so what? They won't be able to break the encryption on [so-and-so-independent service]?". Well, they don't have to. They just have to find someone who is exhibiting a reasonable amount of suspicious behavior and then observe them in other ways or get their associates/family members to flip...Investigations don't succeed or fail based on the unlocking of a key file...it's the work done around the secret that can reveal the secret.
edit: An analogy - You wish to have an affair without your spouse noticing. Since affairs in relationships are not an unheard of occurrence, your spouse isn't going to actively suspect you of it, but he wouldn't ignore signs of an affair either. Having the affair in your own home isn't practical, and you choose not to do it at the Ramada that's just blocks away from your home/workplace because, well, there's so many people there, and there's the possibility that a mutual acquaintance will see you and then tell on you.
So instead, you and your affairee agree to meet each other at a small bed and breakfast that is 1 hour away from your city and so small that no one you know probably even knows about it, and no one at the B&B will care who you are or know who your spouse is.
So are you safe? Well, only until your spouse finds it weird that on occasional days after work, you're driving in a direction that there doesn't seem to be any reason for you to go, and these occasions end up with you being gone for several hours. And in one such occasion, you were noticed carrying what seemed like a bag for a bottle of wine.
By going the obscure route, you've deflected one kind of exposure and opened yourself up to a whole new kind of suspicion.