I like to sympathize with the protagonist, and many times television and books make that impossible. They want me to be on the side of the following characters:
Police who break the rules. Using pain to get information or a confession is the most common TV occurrence of this. Illegal searches because they are justified by the heinous nature of the crime is another example.
People who get into bad situations because they lie. I’m supposed to sympathize with them, but I don’t, unless the lie is very well justified.
Heros who risk the success of saving the world to save a puppy. Yes, that is an exaggeration, but there are many shows and books where the compassion of the hero is shown by how he stops to save a child or a friend when the time may cost him from saving a city. One book I read cited this as a virtue.
People are drug users, crazy, or both. House is an example of this.
People who are rude, immoral, or sleazy. Usually this is portrayed as funny. They break the law, cheat on their spouses, are unkind to underlings, and so on.
I am not suggesting that protagonists shouldn’t have flaws, but I would rather be entertained by stories about decent people.