I'm glad that Bruce Schneier has now had a chance to view some of the primary source documents from the Snowden leaks, because I trust him to speak frankly and I trust his technical ability.
(I'm referring to http://www.schneier.com/blog/archives/2013/09/the_nsa_is_bre..., not the above link).
Both he and Snowden have essentially said that we can still trust the math. Modern symmetric crypto has enough safety margin that even extremely surprising breakthroughs wouldn't give the NSA practical decryption capabilities. (Asymmetric crypto is less certain, but even there Schneier still says discrete-log-based methods with sufficiently large keys are likely ok, and I would bet he's right.)
So the bottom line is this:
- using crypto correctly really matters, because they really are out to get you. Most software gets it wrong, not because there are no good cryptosystems, but because people are ignorant of how to do it right.
- build attack-resistant organizations, not just protocols. The more transparent, flat, and distributed an organization, the harder it is to secretly coerce into cooperating with the NSA. It's a lot harder to force a backdoor into Firefox than into Chrome.
- it turns out open source really matters. The tinfoil hat brigade is vindicated. Closed source vendors really are actively working against their customer's security.