I think it's just you. Do you remember a title character named Charles Foster Kane from a little 1941 picture? How about Rhett Butler in Gone With the Wind? That guy's not your archetypal protagonist.
Hollywood is a broad term, but let's just stick with TV, because that's what this thread is about. In television today, we seem to have one of three production camps. In one, they go for the lowest hanging entertainment fruit - like reality TV, or mindless sitcoms. In another camp are the producers of the crappy, one-hour procedurals that seem to dominate television dramas. These procedural shows all follow the same formula - dead body, smart detective, crime solved, next episode. If that's your cup of tea, then this is Hollywood's Golden Age.
There are other TV producers that endeavor to create something different, something more. In some instances, they pick flawed characters as the protagonist (or anti-protagonist perhaps more appropriately) because such flaws provide fertile ground to explore the complexities of the human condition. Nucky Thompson (based on real life Atlantic city power broker Enoch Johnson), is just such a "anti-protaganist". Not a conventionally "good" guy, but a well-meaning guy who bends (or destroys) the rules to advance what he believes to be the common good.
He has a compromised sense of right and wrong, and it's that very sense that allows the writers to explore the flawed humanity in all of us. In this way, the drama isn't artificially created with the introduction of a corpse in the first scene followed by three acts of mindless exposition, but instead, it's drama that is developed over time with the exploration of the characters and their stories.
This isn't a new entertainment phenomenon. It has been going on since the Greeks, perfected by Shakespeare, and introduced into Hollywood very early on with movies like Citizen Kane. Personally, I'm happy that there are avenues today where excellent story-telling like this is appreciated and cultivated. TV can't all be NCIS - thankfully.
When was the last time you saw even a single hour biopic program on any recent inventor, physician, statesman or any other field? If you go by popular American Media it appears that these people do not exist. Yet in the past, if I may equate 'B' class movies to the HBO / Showtime multi-hour efforts, we had such with Alexander Bell, Louis Pasteur and such.
I reiterate that my complaint is that Hollywood does not seem to see a good America that it desires to portray. The only ones that I can think of quickly involve sports - Secretariat & "The Blind Side". Not to be denigrated but being sold to an already semi-sold niche audience on a relatively non-contreversial subject matter.