Q: You tried to convince him, it has been written, to take your job. Can you tell me a little bit about that what happened?
RC: Shortly after the Bush administration came into office, we were asked to think about how we organized the White House for a number of issues, including cybersecurity, computer security, homeland security, and counterterrorism. I was asked for my advice, and I proposed that the counterterrorism responsibility be broken off be a separate job, and that the cybersecurity job be broken off as a separate job. I said I had done counterterrorism for about a decade, and I wanted to start working on cybersecurity, which I think is terribly important. That was later approved by the president. Link
Clarke didn't think al Qaeda was enough of a problem to keep him in his counterterrorism position.
Color me naive, I didn't think there was a bigger flip flopper than Kerry.