I mostly agree with Booman's take on the issues President Obama faces when dealing with the CIA. But I wouldn't use the word "fear" to describe his position.
The way I see it is that the CIA has been granted the ability to "go rogue" almost since its inception. We give a president 4 or 8 years to turn around a culture that has been embedded there for decades.
So I'm not completely comfortable with what I hear from President Obama about the CIA. But what I am comfortable with is that I know what kind of man our President is...where he's positioned his North Star. And I'm also aware that I don't know the secrets he has to keep.