The issue isn't the fact that the NSA snoops. That's their job and it has value when their power to do so is used judiciously. The problem is that its not being used judiciously. Rather than singling out as few people as possible to root out the bad guys their just collecting everything they can. They don't need to do this and doing so opens up the possibility for huge abuses of power. That's the issue.
I think the article is right that the crypto revelations aren't pertinent to this discussion. I would even consider the crypto revelations a red herring. Is it important how the NSA spies on everyone? No, its only important to know that they do it at all when speaking in the context of how the Snowden leaks are important to creating a national debate and, hopefully, by some miracle, create reforms.
I think its reasonable that as a US citizen you're okay with the NSA being able to break crypto. You just want to be able to trust that they're using it against the bad guys and not you. Even now that we know they're probably using it against innocent civilians its more harmful to the NSA's ability to go after the "bad guys" when they legitimately do (and they still do serve that purpose) and isn't really helping the debate over whether their over collection of data is okay and how to reform that system.