My feeling is that good security measures increase the marginal cost per person surveilled. As the article points out, there are some kinds of communications that Apple is obliged to provide access to. Those are likely to carry low marginal costs per person surveilled, as law enforcement may have the legal means to directly and unilaterally access that information. Even if they don't, the capacity for Apple, telecoms, whoever, to operate in "God mode" with respect to some kinds of communications means that mechanism is a good target for agencies like the NSA to breach.
By contrast, even flawed technologies like iMessage (centralized key management) raise the per-person marginal cost by forcing attacks to be reasonably targeted. While the NSA could probably figure out how to attack Apple's key management infrastructure to set themselves up with a virtual iMessage device for an individual, doing so for all the people would, in principle, be fairly noticeable to Apple.
The more we can instrument technologies that force attacks from "bulk mode" to "targeted," the better chance we have at actually curbing surveillance. Of course, this still leaves the panopticon problem--if we accept that targeted attacks will always be possible, and that any of us could be watched at roughly any time, the psychological chilling effects of surveillance remain.