I don't mean the classical anti-hero, such as Courage the Cowardly Dog, which is a character set on the good side(or neutral at the most cynical), but the complete opposite of that - our Dovakhiin displayes extreme courage, never turns down a challenge, will risk never leaving the Dreamstride, getting backstabbed by Alduin's right-hand man, and in the Dawnguard DLC either not surviving the bite or being soul-trapped. He/she will also join a criminal organization that terrorizes innocents for protection money and respect, steal from innocents, frame them for not keeping their head low, and possibly join a nottrious group of assassins, and either kill the only person to acknowledge them as the rightful leaders of the brotherhood or betray his leader. That's not all - our "hero" is also the leader of a bloodthirsty group who was based on the Falmeri genocide, and depending on his/her allegience, either slays Skyrim's only hope for independance and honor or the protection it now needs the most. He/she also never ever EVER turn down a daedric quest, as foul as it may be, Boethiah's Calling & The Whispering Door being two of the most prominent examples. Paarthurnax even states that the dragonborn has an inborn desire for power, and that he himself could only overcome his nature through constant meditation and following the Way ot the Voice.

It made me ask myself, are "good" players, who refuse to follow up to "evil" quests and quests lines, actually breaking out of character? Are they giving their OC's more moral credit than they should? Is it supposed to make us question our decisions when playing a game as someone else, or to show us that we don't have as much control on our characters as we would like to think?

One guild a play-through, unless I role-play

The player gets to decide if he is evil or not. You could easily tell Meridia where to go in the whispering door quest and went on your way.

I don't like to see it as 'good' and 'evil', seems a little too basic. I'm fine with being in The Companions and The Dark Brotherhood, neither is morally better than the other but simply two different ways of earning a living in a land abundant with possible world-ending hazards.

A Dragonborn can choose to do good quests for selfish reasons as well (like trying to make everyone see him as a hero figure and thus turn them into assets he could use).
I do agree however that Dragonborn being an ambitious bastard is more fitting than being a goodie-two-shoes. All Dragonborn we know were either evil or evil at some point of their life (before Jagar's plot, Uriel was not exactly a kind person and Martin was a Daedra Worshipper thirsty for power... Talos was an backstabbig warlord until his death).
Of course, he can always follow the Way of the Voice. If it can heal Paarth, it can him as well.

It is also my personal canon that with every absorbed soul my character becomes nastier and has less qualms to do things for selfish reasons.

Also, TES ain't exactly a Good Vs. Evil universe so just do what you want.

Courage the Cowardly Dog is the classic example of an anti-hero? O.o?

Maybe the classic example of a reluctant hero, but not an anti-hero.

To answer your question, the Dragonborn is tabula rasa. (S)He is what you make him/her. The Dragonborn can be a pillar of integrity and virtue, or a scheming lowlife who kills people without hesitation just for amusemant.

Yeah. I bet you he could have saved the farmer all those times, but he just refuses to out of spite. What a rotten dog...

All I did on the whispering door quest was take a key. Wasn't bad. I know I could have killed someone, but that was easier.

I roleplay so it is never about the player, it is about the character. The roleplayer is not "good" or "evil," the character is.

Some of my characters do bad things, some of my characters do good things. Some of my character walk a line in between good and bad actions. So, as a roleplayer, I am never forced to "break out of character."

This.

From a canonical standpoint, the Nerevarine or the Champion of Cyrodiil didn't do every single quest, as far as I know. It's never confirmed. Same for Fallout 3 (except for the Wasteland Survival Guide, assuming the Lone Wanderer is the only person who would've helped). Bethesda has made a point of ensuring players don't feel their characters are supposed to be a certain role or do certain quests. I would't really call the Dragonborn an antihero. It depends on the specific Dragonborn, just as it depended upon the specific Nerevarine or Champion.

As Todd pointed out in his demo video, one could do a bit of this, a bit of that.. or they could do the main quest to be a hero. I forgot his exact words, but he thought of it as heroic. I think there's a hint from writers when you first hit Whiterun too. If you talk to Jon Battle-Born, and say you're there to help.. he says go to Jarl, he can set you on the right path. It's basically pointing you to a "good" sort of quest. You can choose to avoid just about anything else -- granted, it's tough.. sometimes you'll do questionable things by accident, but being a "hero" is possible. Kind of. You don't have to do everything on one character. Makes no narrative sense anyways. Imagine reading a novel where one character did all of that. People would laugh at that story.. it'd be beyond stupid.

One thing I liked about Fallout 3 was that it had clearly delineated good and evil. Even if you didn't agree with its definition (for instance that virtual mass-murder was an atrocity but actual mass-murder a good thing), but it allowed you the power to be a hero or a monster. New Vegas was a bit more compromised, since even the "good" faction(s) required you to commit certain evil acts.

Still, in Skyrim, you have tremendous power of choice. If you don't like the Dark Brotherhood, you can decline their invitation or eliminate them. You can also refuse to join the thieves guild, even though the recruiter and the town's crime boss are both essential. And RP-wise, you can end the Civil War quest with the truce in the Main Quest. And there are any number of people you can help. Since there is no karma system, there are fewer intangible rewards for playing a good character. It can, however, be done.

yeah the "generic" dragonborn is a [censored], leader of all guilds including the thieves and dark brotherhood, hell in the dawngaurd trailer he even becomes a vampire lord. Although your dragonborn doesn't have to be an evil [censored], the evil [censored] questlines still get completed

In this same vein of thought the coc is the new madgod, listener, grey fox, archmage, and fighter's guild head

the nerevarine also most likely completed every possible questline (and yes i know that isn't really possible, but the majority of them can be completed on one playthrough)

And in future tes games the worst is always assumed to have happened on any questline with a good/bad ending, remember raven rock failing in the oblivion pvssyr?