Its DHS that is responsible for protecting critical infrastructure, not the NSA:

http://www.dhs.gov/homeland-security-presidential-directive-...

In the NSAs charter, the term "National security information" refers to classified information and "sensitive but unclassified" information, and the scope includes those systems. The scope does not include protecting all systems that might have national security implications, the NSA has no regulatory authority or requirement to do this.