To make your question short, and to see if I understood it correctly, we're talking about a player who made his character a certain one and roleplays it entirely different. You added that you think that it comes from inexperience, and that he created this character after you said "no" to some "freak-character"-ideas. You want to help him roleplay the character he created.
As I see it, this problem is made from two smaller ones. The first is that he doesn't see his character as interesting because the character "is normal and normal is boring". The second is that you wanna help him understand why the way he plays the character does not fit the story-world of your game.
Helping him understand that "normal is not boring
This is the more important problem, as it stands in the basis of the entire problem. If he'll see that normal characters can be interesting his "anti-persona" will perish and he'll roleplay a normal character and not a freak one. The main trick here is to show him that normal characters are not entirely normal, i.e. "no person is like the others". In order for that to work, we need to give the character depth.
The easiest way to give depth to a character is through internal conflicts. Having goals and all is nice, but without something that blocks oneself from achieving them it is far less interesting. First thing to do is to go over his character's background and see if he implemented there an internal conflict for his character. If so, show it to him and talk with him about it. If no, sit with him and help him to come with one. The internal conflict doesn't have to be extravagant, but it needs to be there. An example one might be that he loves Vincent's sister but secretly hates Vincent himself, or another like Loves the sister but thinks that he's not good enough for there. I'll take the second one as an example for this section.
The conflict gives us a few things, a few added benefits. It gives the character 2 conflicting goals: "Get the sister and prove that I'm worthy". Now, with those two we also get a kind of an achieving-plan: "If I'll show her that I'm worthy, by getting something amazing done, she'll want me and I'll be able to get her". More than that, the character gets the knowledge that each advancement in order to achieve one goal will drive the other one to the far end.
But the first conflict is even more interesting. The character here has the knowledge that he needs the brother in order to save his lover, but he just can't stand being near the brother. He'll drive the mission onward for two reasons but he'll have doubts about his lover- if he'll marry her he'll be stuck with this brother of hers.
To make long story short, simple conflicts can show the player that even normal characters are interesting and unique. When combined with goals they force the character to take certain steps along the roads, to commit certain actions along the way, that he won't want to do but will make him doubt himself and question himself and see that his problem are far more interesting than those of every freak that he'll encounter.
Another nice way to help him see the importance of conflict is through showing him and analyzing with him certain protagonists that are normal people, from the stories and movies and series (of any form)that he likes. He'll see quite quickly that the conflicts make them interesting.
But he may say that it is not enough. For that there are a few more literary tools that might help him see why normal people are interesting. The first one is having flaws (internal or external) and the second one is using "The Ghost".
Flawed characters are characters that just like normal people aren't perfect. Those flaws can be internal (self-doubts, for example, or a mild paranoia) or they can be external (they're look frightens ordinary people, for once, or a missing hand for the other). The idea is that the character has to deal with the flaw, and one day to find the strength to overcome it. The fight for the overcoming act makes the character far more interesting. A nice example of that can be seen in The Rain Man, where he learns at the end that he can count on strangers/"dumb" persons like he's brother. Another nice example can be seen in the story of The Ugly Duckling who although looking terrible learned to acknowledge himself and to accept the way he looks, to accept his difference.
"The Ghost" is an event from the past that just like a ghost haunts the character to this day. Again, trying to cope with it is what builds a deep character. One example for this can be seen in the movie Inception, where we literally have a ghost- Cob's wife. Another example for this can be seen in the movie Casablanca, where he has to deal with his broken relationship with Ilsa. This Ghost is far more interesting as the originator of the Ghost actually comes back to his life. In Frozen we see another kind of a Ghost- the act that one feels guilty about. Elsa actually killed her sister.
All of these techniques are there for one reason- to make regular people interesting, to give depth to the characters, to make them human beings with goals and drives and psychology.
Helping him see that his character doesn't fit the world
After he understands that he doesn't have to be a freak in order to be interesting, he will be far more understandable about playing a character that fits the world. Then, try to explain to him as calmly as you can what it is in the way he played his character that doesn’t fit the world.
Explain to him that the characters are in a world where being a freak is bad, where achieving one's goals is the ideal. Each and every one for himself, as the saying goes. Give him examples from the way he played his character and analyze with him, in a one-on-one conversation where his way of acting came from. Use the background he created to illustrate to him where your problem comes from.
Then ask him what problems he has with his character, and together try to find a solution. Maybe let him be just a little bit freakish. Maybe he needs to just create a different character. This is basically between you and him. After that show the updated character to the group and get their approval.
When combining those two, you'll get a player who his far more willing to both play the character while also seeing the problems with the way he played his character before.
Combining the two solutions
When combining the two solutions you get a better player, who understands for the future also how to create regular characters that are not freaks yet far more interesting than those freaks will ever be able to be. Furthermore, you get a player who is willing to play his character as written while still making the character fit into the world. Hope any of these helped you.
(There are some great answers here. I want to suggest that Bob's style can be reframed as a positive.)
Encourage growth in Bob's character's anti-authoritarianism
It seems to me that one way of thinking about Bob's anti-authoritarian style of play, is that the meaning of the anti-authoritarianism is not being woven into the game. Anti-authoritarianism comes in many flavors and historical/cultural contexts (e.g. punk and anti-facism, futurism, 21st century social anarchism, nihlism, DIY/DIT, etc.). While you have noted the my way or the highway action-hero style of Bob's playing, it is possible to encourage his growth and investment in anti-authoritarian motivations, philosophies, in-game allies and the like:
Both the GM and Bob might benefit from one-on-one discussions investigating his character's motivations for anti-authoritarianism. This could even lead to developing story arcs that deepen, evolve or resolve the character's issues with authority. Maybe Bob might come to appreciate different approaches to anti-authoritarian play?
The GM could introduce anti-authoritarian NPCs. Such characters could be introduced in a manner that dramatically highlights their screw-the-man! tendencies in a way that earns Bob's appreciation, while at the same time drawing tension with Bob's character because their philosophy, style, or motivation differ from Bob's character's own. For example, an anti-royalist anarcho-syndicalist NPC might scoff at Bob's anti-mutualist it's-all-about-me style, while Bob just thinks they way they oppose the Royal Court is the coolest thing. This pattern can also be inverted if, for example, Bob's character is deeply put off by, say, destroy-the-world style anti-authoritarianism his character may be forced to examine the uncomfortable ways his own methods and motivations align with some seriously evil nihlist's.
The GM can embrace Bob's anti-authoritarianism as an ideal for NPCs to emulate. Bob's character's actions may have a broader social import that shapes the culture and plot of the game setting. For example, "Did you hear the news? That new group of fighters used a thermal detonator on Chief Wookiebusiness! We are finally out from underneath that bastard's grasp! Let's roll this into a coup of the corrupt regional boss Wookiemonster!"
Of course, Bob could be just a bad fit for your group... but optimism, hey?
Obligatory Monte Python & the Holy Grail quote:
Arthur: Well we all are! We are all Britons! And I am your king.
Woman: I didn't know we 'ad a king! I thought we were an autonomous collective.
Man: (mad) You're fooling yourself! We're living in a dictatorship! A self-perpetuating autocracy in which the working classes--
Best Answer
I've come across a similar issue where every character the player created became annoying to the other players, sometimes right away, sometimes after a short while. As it turned out, the problem wasn't the one player, it was all the other players. You see, because his first character had annoyed them, they started to treat all his characters the same way and this led to his other characters reverting into the annoying character he originally played. The worst part was, no-one realised that this was the reality of what was happening until we all sat down over a pint of beer in the pub and discussed the issue. It never completely resolved itself (there are still a couple of players who just can't stop acting as though his character is annoying them) but it did get better.
Perhaps your guys problem is in fact similar to the above. If so, I'd suggest you all discuss openly. As the saying goes "first impressions last" and in this case, that proved to be more true than we would have thought.