In my opinion, the protagonist is Victor Frankenstein. He created what he believed would be his best work, what would shatter the laws of nature and arouse the interest of all to see. Instead, he created a monster...literally. His entire plan backfired on him, and to some extent, I think he knew that terrible things were going to happen when he saw the monsters face. Most people tend to think that he feared the monster because it was ugly, however it is possible that he could see the monsters evil in its eyes, the windows to the soul. After causing him much grief, and the many deaths of his loved ones, the monster finally gets Victor to take action. He swears to devote his life to hunting the monster through the world, and killing it. Frankenstein did not want to cause any deaths, but when he realized what had been done and had been pushed to the point of nothing to lose, he began his quest to end the madness.
He set off to slay the true antagonist, and that's where he met Captain Walton.