As a genre, Gothic literature tends to reflect the presiding fears of the society in which it is written. This is certainly true of Frankenstein, whose primary concern is one we see elsewhere in works from the Enlightenment era: that science was evolving too quickly for humans to deal with, with the result that people were beginning to think they could, effectively, become gods.
In this novel, the subtitle "The Modern Prometheus" points the reader to its central thesis. The story of Prometheus is a cautionary tale of a man who thought he knew better than the gods, and, indeed, that he could relate to humanity just as well as they could, provided he had the right equipment. But the fire Prometheus stole was the preserve of the gods for a reason; and they kept it from humanity for a reason, too. In the case of Victor Frankenstein, then, the fear expressed is not that science will turn us into gods; rather, it is that science will make us egocentric enough to believe that our advanced technology makes us equal to gods, whereas, in fact, this is pure hubris.
Victor is not at all equipped to handle the creature he births. His knowledge of science may have permitted him to create life, but he does not know how to relate to or nurture that life; he expected to create a docile being who would respond to him, but in actuality, creates a thinking, feeling, willful, and sorrowful being, suicidal because he knows he is too different and too imperfectly made to ever have the companionship he needs. His personality is human; his external aspect is monstrous. But the monstrosity is not a reflection of the creature himself; rather, it reflects the hubris of Victor's creation, and is evidence that he used his technology too soon, before he had thought through its consequences.
In building the Creature, Victor essentially causes his own demise, as well as the suffering and painful death of a feeling entity who should never have been born. The suggestion here is not that science is inherently bad, but rather, that it has the potentially to be used very badly by people whose pride and ego outstrips their common sense and understanding of their own limitations.