One of the possible reasons why this trope is so common is because Science by itself seems to make a lot of artistic tropes or stories irrelevant. Another possibility is the fact that science pushes technology forward which forces Hollywood or such to adapt which it doesn't appreciate doing. Finally the other issue with science is bad is that it's easy. Merely showing the simplicity of the message means that it's very easy to villainize it.
It may also be that some religious people see science as the opposite number of/threat to their religion and think that it's a "belief" or even "a religion" that's opposing them, due to some conflicts over theories like evolution (though a lot of the conflict has been overblown or fabricated too). A common lament too is not so much against science, but its results being technologies which are used or misused to create dangerous things (i.e. nuclear weapons). In some cases, this turns into a broader anti-science sentiment. Postmodern criticism of science stemmed from this.
In general, this and Magic Is Evil strongly overlap due to a perceived common threat to a religious status quo. Many tropes historically associated with evil magic (abominations, Immortality Immorality, evil social outcasts) see a continuation with demonisations of science, and unsurprisingly some of the oldest examples are alchemists and "wise men" disliked by Christian religious authorities.
