Doc,OK, imagine a confrontation between a human armed only with a toolbox and a present-day ICBM armed with several thermonuclear MIRV warheads, but without any human intelligence to initiate or guide any action.
I'd bet on the human with the toolbox as being more likely to survive the confrontation intact.
Even if we start talking about far-future technology, there is no guarantee that trans-human artificial intelligence is possible. It may be possible to create the hardware capable of sustaining such an intelligence, but unless humans are capable of designing the software for an intelligence greater than their own (or designing the software capable of creating such software, recursively), then trans-human intelligence will remain impossible.
Even if it is possible, problems with the earliest AI's may lead to prohibiting the creation of such entities.
So while it is possible the human brain may become completely obsolete, it is not inevitable.
As for edge-of-the-envelope spaceflight, technology may allow humans to tolerate far more than they can now. After all, if we're talking about a civilization with FTL travel, there's no reason they might not have inertial compensators and artificial gravity. In David Weber's Honor Harrington series, the humans don't even blink at the idea of manned warships accelerating at hundreds of gees.
Similarly, technology can shield humans from near-misses by weapons such as nukes, grasers, and antimatter warheads.