We have a biological imperative, a survival instinct to fear that which is inhuman.
The most frequent use of monsters in fiction is that of a challenge for the hero to overcome, a foe to vanquish. If the hero of most stories is a proxy for the audience then defeating the monster is our vicarious triumph over our phobias.
Ocasionaly though, the monster’s role in fiction is reversed. Sometimes the monster is the hero and even though the concept may not have originated there, no where is it as prevalent as it is in the world of comic books.
The Incredible Hulk, Swamp Thing, Hellboy, and Etrigan the Demon would all fit easily into the role of villain in any traditional story. Stan Lee, Len Wein, Mike Mignola and Jack Kirby respectively decided instead to make their fiendish creations into good guys. Why would these creators and others like them who work in a medium practically defined by it’s heroes decide to turn the concept of monsters on it’s head?
For one thing we as a species have overcome many biological imperatives in our ongoing quest to put learned behaviors over instinctual ones. It is no longer acceptable behavior to base our fear or judgement of 
others on superficial traits. The Fantastic Four ‘ s Thing may be a horrific mass of craggy orange rock instead of flesh and bone but he has a heart of gold. For another, the heroic “Knight In Shining Armor” has never been a valid proxy for most people as most people are lacking in the virtues that signify a classic hero. We being quick tempered or prone to petty emotions such as envy or revenge probably have more in common with the dragon or evil witch. In short we relate to monsters better because we are imperfect.
Who is easier for the average person to identify with : Superman 
with his impossible good looks and godlike abilities, or the Incredible Hulk who perfectly represents man’s struggle between the Id and the Super-ego ? Who hasn’t dreamt of uttering “Hulk Smash!” While destroying everything and everyone that’s annoying them ?
Monsters as heroes also help to demonstrate to us that it is possible to overcome our nature. Both Hellboy and Etrigan are demons born in universes where the concept of hell is all too real. The two have worked hard to not follow in Satan’s footsteps despite having been told that they are evil solely based on parentage. And yet, both have chosen to fight for the forces of good. To ignore their so called “destiny” and make their own way.
So many superheroes are impossible to identify with. The majority are drawn as Adonis ‘ s with perfectly chiseled features and muscles (or curves if it’s a female hero) that go on for days. Even Peter Parker supposedly the most relatable hero with his realistic problems and challenges is still hot enough to get married to a super model.
On the other hand someone like Nightcrawler who is shunned by normal society for his demonic visage is a little bit easier to commiserate with. Not that there are many fuzzy blue elves walking around reading X-Men but surely the book has been picked up by an outcast or two.
Monsters will never replace dashing leading men or buxom heroines as the go to protagonists in comics, literature and film but as long as there are freaks, outcasts and anyone else who doesn’t fit into societies definition of normal there will be heroic monsters to represent them.
