No evidence in the article substantiates this bold statement.
- "pressuring major Internet firms to provide their "master" SSL keys for government surveillance purposes": this demonstrates a weakness of centralized public-key infrastructures, it does not follow that public-key cryptography is doomed. (See: web of trust.)
- wiretaps, snooping, etc.: everyone is welcome to grab a copy of the ciphertext, this does not prove that cryptography is futile -- quite the contrary.
- "concerns about the security of widely used cipher algorithms and a range of other associated exploits": vague.
- "it is prudent to at least assume that intelligence agencies around the globe may still be working several steps ahead of public "state of the art" in crypto tech": unfalsifiable.
- "forced the hands of chip manufacturers to include "special goodies" for surveillance purposes": I am willing to fear deliberate plausibly deniable weaknesses on accelerated hardware implementation of crypto primitives, e.g., PRNGs, but it seems very hard to believe that implementations of public-key crypto using general purpose instructions could be somehow identified by the CPU and somehow tampered with in a way which would be non-obvious somehow.
- "when governments really want to target someone, they'll find some way to compromise the associated computers directly -- either through phishing or other malware attacks, or via in-person "black bag" jobs to physically alter systems as they might feel appropriate": humans are the weakest part of cryptosystems, and if they have physical access then they win; nothing new here.
In conclusion:
> I believe it would be fully appropriate for us to be considering alternative methodologies for data protection that are sufficiently outside the existing public-key "box"
Public-key cryptography is a tool. It certainly does not form, in itself, a full "methodology for data protection", but nothing in the article justifies that has lost any usefulness in its current form.