Controversial Httyd opinion:
The only thing that kept Valka from being treated like a witch, and Hiccup from being drowned at birth and or exiled was Stoick. Heck Stoick's right hand man and confident/only person allowed to question him was Gobber, a gay man! I don't think Stoick really truly has a problem with Hiccup being different. Stoick continues to surround himself and love people who are different. I think what really made him the way he is in the first movie was the pressures of being Chief and losing Valka. This fear that the village doesn't respect/hates Hiccup, mixed with the fear of losing the last bit of family he has left to the same monsters that took his wife. So he becomes obessesed with his son needing to fit in, be like everyone else for Hiccup's own safety. From the flashbacks we saw of baby Hiccup and Stoick, he and Hiccup had a good relationship. It's just eventually the village's criticism and fear, plus the dragon attacks filled Stoick with fear and need to over protect his son.
