His resignation letter cites problems with OMB, DHS (presumably NPPD), and NSA. The press seems to be covering the NSA criticism most closely, though I suspect his frustration was driven as much by the funding and organizational issues as by NSA:
Former Silicon Valley entrepreneur Rod Beckstrom said in a resignation letter published by the Wall Street Journal it was a "bad strategy" to have the National Security Agency, which is part of the Department of Defense, play a major role in cybersecurity.Rod is a friend and a remarkable talent. He understood Washington much better than most in Silicon Valley. His inability to move the bureaucracy shows how deep is the divide between government and the tech community.