If we think about our ancestors, not the apes, or the Homo Erectus but the Greek and Roman empires, or the people in B.C who were learned enough to have civilizations. I'm not very clued up on history. So anyway, you can see why these particular people would take solace in religion rather than trying to comprehend the vast magnitude of the history of the human race.
However, whilst the fear of the music and comprehension of insignificance is still fresh, the movie throws us a curveball in the form of the HAL 9000. The film really shines here by showing us about three different forms of terror at once, and combining them to make you metaphorically shit your pants with fear. I think I'm going to separate these into different examples so that everybody, even the stupidest of Gods creatures.
The First Kind...
The terror of the H.A.L 9000.
Not just as an unstoppable machine thing, but as the complete conglomerate of all human knowledge. The fact that when all human knowledge is combined, the only logical option is the destruction of the human race is a truly horrible thing, but it is especially bad when a creepy robot saying "I cant let you do that Dave" is enough to give you the willies.
The Second Kind...
Mans battle against space.
The movie sets in early on how un-designed for space humans really are, with ridiculous contraptions made for helping us all to survive the vacuum of space, and with every slightest little thing, even walking, being a gigantic problem, but the best representation of this is the spacewalk. This scene shows the two crew members dave is with die horribly by suffocation, which as horrible as it is, when described as a "necessary action" by a machine that contains human logic is even worse.
The very first scene of space travel shows the most poignant image of this, with the stewardess of a commercial space flight struggling to walk without the aid of special velcro shoes. However, it also shows how humans have adapted, perhaps calling back to the very start of the movie with the Homo-Erectus using tools. When the Homo-Erectus discovered it could use the bone to its advantage, or more specifically, to beat the shit out of things, it discovered technology. The technology is all around them in the spacecraft showing how the technology is becoming insignificant, or rather that we as a race have evolved as far as we can.
The Third Kind...
Overcoming humanity.
The third kind of fear ironically also features HAL. The penultimate scene, where our intrepid hero Dave has to destroy the HAL 9000 computer, for fear that it will kill him is more of a commentary on how we must overcome humanity in order to evolve. Coincidentally, Dave evolves after this into the "Star Child", and not the KISS version. Because that would be weird. The scene juxtaposes HAL's attempt at reasoning with the heavy worried breathing of Dave, showing how truly vulnerable Dave is to the cold, calculating logic of HAL. And also space. When HAL is destroyed, he is de-evolved almost exactly. He first becomes defensive, then frightened, the reasons more, claiming he's "better now". After this comes the song, which HAL sings, with an increasingly lower voice, his tone shifting from the cold monotone educated, to the almost grunt-like Charlie Brown teacher voice. This could perhaps be construed as a representation of true de-evolution in the last throes of HAL's life, with the low-tone grunts being sort of like the grunts of the pre-Homo-Sapien life forms at the start of the movie.
I just got chills...