We are a long, long way from eliminating mystery from the world. Even in as reductively complete a case as QM, there seems to be no end to the mystery. My personal favorite is the electron that can tell the orientation of a magnetic field even though it is excluded from the region of the field. Another cool one is the bomb detector that uses light to detect a light-activated bomb.
In fact, one can argue that mystery can never be eliminated entirely because every scientific theory must have axioms and undefined terms.
BYW, my feeling is that Dawkins doesn't have an agenda per se, merely an intense and irrational dislike for religion. One often sees the reciprocal dislike for irreligion on these threads.
Anti-religion