The threat today is Al Qaeda. How bout tomorrow? The threat is basically arbitrarily defined by the government. Whether your secrets are worth listening in on, well that depends a lot on what the government perceives as a threat.

Edit: Also as far as the separation of powers goes, that doesn't mean the executive branch operates independent of the other branches. The executive branch still has to comply with the laws made by the legislative branch and the rulings made by the judicial branch.