For the most part, the theme of knowledge is portrayed as being negative in Mary Shelley's Frankenstein. While the initial quest for knowledge does not seem to be harmful, for either the characters in the novel or the reader, once the novel's actions are set in motion, the quest for knowledge becomes apparently negative.
In the beginning of the novel, readers are introduced to Walton. Walton is on a quest for knowledge--he wishes to find the seat of magnetism at the North Pole. Undaunted, Walton is willing to risk his life in order to reach the pole. By the end of the novel, after hearing Victor's tale and warning about ambition ("Farewell, Walton! Seek happiness in tranquillity and avoid ambition, even if it be only the apparently innocent one of distinguishing yourself in science and discoveries."), Walton is willing to give up his dreams and return to England.
It is past; I am returning to England. I have lost my hopes of utility and glory.
As the narrative moves over to Victor's tale, knowledge is shown in very negative light. Victor, admitting the power of seeking knowledge, gives advice to Walton about the negative aspects of the quest. Here, Victor admits the poisonous nature of knowledge.
You seek for knowledge and wisdom, as I once did; and I ardently hope that the gratification of your wishes may not be a serpent to sting you, as mine has been...Learn from me, if not by my precepts, at least by my example, how dangerous is the acquirement of knowledge.
While much of the negative aspects of knowledge are blatant in nature, like the quotes above, some of the negative aspects of nature must be inferred by the reader. For example, the creature desires nothing more than to know who he is and where he comes from. Upon gaining this knowledge, the creature seems to regret acquiring the knowledge of his birth.
Everything is related in them which bears reference to my accursed origin; the whole detail of that series of disgusting circumstances which produced it is set in view; the minutest description of my odious and loathsome person is given, in language which painted your own horrors and rendered mine indelible. I sickened as I read.
Based upon these passages and quotes, one can see that the overall theme of knowledge is negative. While the initial quest for knowledge seems innocent enough, the outcome for all of the "men" is overwhelmingly negative.