Well I do believe on one hand it's a matter of typical american culture "fearing intelligence", or to some extent the way american religiosity is at war with science. However the thing is, the "science gone bad" trope appears in other countries too, including europe. Hell even here in sweden. Religious people in sweden usually put full trust in science, and we're a generally science-positive country.
The side I think is being forgotten here is not the fear of science, but rather the fear of what humanity's curiosity might bring them. A curiosity killed the cat kind of thing.
I pose this to you:
Science gave us the atomic bomb.
Science gave us the vehicles that are slowly killing the nature we depend on.
Science gave us tools with which we can more effectively oppress each other.
Science has been used to oppress minorities.
People have a lot of curiosity about what science can bring us, but also a lot of fear. For good reason. Science is an amazing tool in the right hands, and a deadly weapon in the wrong hands. This is probably why story creators are so fascinated by the idea.