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order is probably because Executive Order 12472 (which established the National Communication System) has become quite out of date, particularly because that EO detailed telephone communications while this one details more general cyber-security issues.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.
It's a lot more complicated than anybody can possibly imagine, and it's probably why the Obama administration has given NSA's General Alexander so much backing in recent spying revelations.
In addition to the spying revelations, there has been concerns about the US Government's ability to manage and maintain confidentiality, integrity, and accessibility of critical communications in case of major and sustained attacks on its communications infrastructure.
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.