The real purpose of this order is probably because Executive Order 12472 (which established the National Communication System) has become quite out of date, particularly because that EO detailed telephone communications while this one details more general cyber-security issues.

The NCS was a department that was absorbed into the DHS and this EO effectively puts the NCS to an end.

See more:

http://www.dhs.gov/office-cybersecurity-and-communications

http://en.wikipedia.org/wiki/National_Cyber_Security_Divisio...

This EO is simply a formality, rather than some dangerous encroachment or commandeering of the internet's infrastructure.