Still the majority of the plots are still focused on Kirk throughout the series.
Yes, indeed Kirk is the protagonist. It is his goals we want to see realized, his success we root for. Kirk and Spock are like two halves of one whole. And when you add in McCoy you get a fully realized trinity. McCoy=emotion, Spock=logic, and Kirk=faith as he relies on the advice he gets from the other two. And Scotty=doubt of course! "We can't do it Captain! I need more power!"