Something which rumbles is both unsettling and unsettled. By it's nature, it's unstable - in constant turmoil.
So you refer both to the unstable thing - the storm; the earthquake - and to it's unstabilizing effect on you.
When we try to describe the conscious and the unconscious we usually end up using metaphors, because we're only just beginning to truly understand the mechanics of it.
He's saying that the fear of death has both conscious and unconscious aspects, and that it often hovers on the brink between the two. (You see, I'm doing the same thing!) The instability of it causes it to unexpectedly burst into our consciousness, and then return to the unconscious.
"Under the surface of our minds" is argumentative, because we usually say our "minds" comprise both the conscious and the unconscious, the latter being "under the surface," so to speak.