(note: if you haven't watched this show, and intend to, don't read this. Spoilers and all).
Who is Deadwood's protagonist? Let us look at the options.
Seth Bullock: the most likely candidate. He's the first central character to appear on the show, he shows up in Deadwood when we do, he's repeatedly shown courage and morality, and (don't underestimate this) he's good looking, clean, and clean-shaven. However, he's a minor character in much of the plot that has occurred--there are episodes in which he barely shows up.
Sol Star: He's too much the "best friend to the protagonist" role to be a protagonist.
Al Swearengen: This is an evil man. He's selfish and violent. He steals, cheats, and murders. And yet, HE is the one the show focuses on most. It is his schemes and desires that are at the heart of most of the show's plot. Is he the protagonist as anti-hero? I suppose it works.
Mrs. Garrett: Her husband is killed too quickly to be a protagonist, but Mrs. Garrett works as one. BUT...she'll have to develop into a more prominent character for me to consider her the protagonist.
Anybody at the Bella Union: They showed up several episodes in; no protagonists there, though they are now central characters.
Wild Bill Hickock, Calamity Jane, Charly Utter: Because Bill is killed so early, and Jane and Utter (despite being likeable, moral characters) play too much the role of supporting friends, I don't see them as protagonists (am I too dependent on conventional notions of clean, good looking, well-spoken protagonists?).
Doc: Now HERE's a real possibility. He's twitchy, scraggly, and hunched over. However, he's constantly involved, and he's shown intelligence, cunning, courage, selflessness, and morality. He moves about like he's a shady character, but in all of his actions he is downright heroic.
Those are the possibilities. The other characters (Trixie, E.B., Dan) are suboordinate to more important characters. We'll see how the Bella Union people develop. Right now it appears the possible protagonists are Swearengen (evil, selfish, and murderous), Bullock (protagonist in all but centrality to the plot), Doc (protagonist in all but appearance), and Mrs. Garrett (who is becoming more and more central to the events, character development, and plot).