The biggest thing I can think of to illustrate this right now is Pirates of the Caribbean. Will and Elizabeth start out as ordinary colonists, well, Elizabeth is the governor's daughter. They are good. Will is a blacksmith. He hates pirates because they are criminals. Throughout the course of the story, both Will and Elizabeth become pirates. They gradually lose their moral compass, learning to do whatever it takes to accomplish what they want to. True, the British officers aren't really good guys either, but that doesn't mean that it should be okay for the "good guys" to be pirates.
Now, I enjoy Pirates of the Caribbean (not the fourth one, I hated the fourth one), but the lack of a true moral compass by any of the characters annoys me. For instance, in the second movie, Jack Sparrow wants to get out of dying yet again, so he and his crew try to round up one hundred people to unknowingly send to their deaths, so as to trade one hundred souls for Jack's life. Am I supposed to support that? Maybe not, but I don't remember the movie making it clear that it was the wrong choice. SPOILER Elizabeth ended up tethering Jack to the Black Pearl so Davy Jones's beastie would eat him, thus killing him and alleviating the need to kill one hundred souls. So they didn't actually go through with it. Then they went to Davy Jones's Locker to get Jack out, cheating death once again. END SPOILER
Another thing that bothers me is NBC's Revolution, which has now been cancelled. I watched the first half of the first season, and enjoyed how Charlie was a good person in the midst of chaos where everyone, including her uncle Miles, were willing to kill for any reason. I stopped caring about the show when it came back after Christmas because they killed off Charlie's brother Danny, who they were trying to rescue for the first half of the season. Then they started adding in inappropriate material and I really really didn't care to watch. But my parents still watched the show, and so occasionally I caught part of an episode. I was disappointed to see how all the characters had deteriorated into wandering around killing people without much purpose. Sure, maybe Charlie and Aaron were wimps at the beginning and needed to toughen up, but to become killers? Maybe that's part of the reason why it was cancelled.
Yet another is National Treasure. I enjoy it and its sequel, yes, but the characters constantly break the law, nonchalantly, and get away with it. They steal the Declaration of Independence, kidnap the President, hack into security systems, break into numerous places, and Ben Gates even once remarks, "Maybe one day I'll wear this to a party I'm actually invited to." Somehow they're the good guys, I suppose because they're not going around shooting people. Still, every time they get off scot-free, and are hailed as heroes for the historical finds they made in the process. It's "the end justifies the means" in action, and I don't really think that's a good message to be sending people.
I suppose Star Wars is a different matter, since the prequel trilogy is a story about how Anakin Skywalker became Darth Vader. His behavior isn't condoned. It tears everything apart, his friendships, his marriage, the Jedi Order, the Republic, the entire galaxy. This is a place where a negative character arc is necessary and well done. (Yes, there are tons of flaws in the film-making, but I think the negative character arc was well done.) I still don't see why Padme was stupid enough to marry him, when she knew how bad he could be, but someone had to be Luke and Leia's mother. I don't agree with the idea of marrying someone in hopes of reforming him, but again, someone had to be Luke and Leia's mother.
Something I like about Tangled, one of the many things (yes, I'm now an adult and I love that movie), is that Rapunzel didn't really start falling in love with Flynn until he saw the error of his thieving ways and started trying to be a hero. At the end Flynn says specifically that he gave up thieving and turned his life completely around, then it says that he and Rapunzel got married. See, just as I think it's bad for girls to expect perfection from their future husband, I think it's dangerous to make them think they can marry someone bad and reform him to make him good. The song "Fixer Upper" from Frozen interestingly points this out:
"We're not saying you can change him,
Cause people don't really change.
We're only saying that love's a force
That's powerful and strange.
People make bad choices when they're mad or scared or stressed.
Throw a little love their way,
And you'll bring out their best."
People can change for the better, but it's not a good idea to marry someone in the hopes of changing him. That isn't likely to work out well. It's more likely to deteriorate into a really bad situation. There's a reason the Bible says Christians shouldn't be unequally yoked with non-Christians.
Bryan Davis is actually very good at creating good, but flawed characters. Jason Masters from Dragons of Starlight and Nathan Sheppard from Echoes From the Edge are both gentlemen who care about the people around them and try to do what's right. They have flaws, but they are things they struggle against in order to do right.
I'll finish with Bardon from the Dragon Keeper Chronicles again. He is a good character who is a gentleman and a knight, but he has flaws. Yet his flaws are not condoned. Kale doesn't think it a good thing that he constantly gripes when riding horses instead of dragons, though it does amuse her. Make good guys good. Don't make them perfect, give them flaws that are clearly portrayed as flaws, and make them good. Well rounded characters are the true key to an excellent story.