In Kirk's case, moreover, the script has him simply taking over and then alternating between making bad decisions (the wormhole scene) and making none at all.
Kirk rushing the Enterprise arguably led to the transporter accident.
I agree with you that Spock really is the protagonist, though, and Kirk is more of a supporting actor. Spock is the character who makes all the breakthroughs in understanding V'Ger. Everyone else just reacts to this.
The closest Kirk comes to steering the plot is his verbal sparring with the Ilia probe. Kirk merely uses the insights gained from Spock to decide how to communicate to V'Ger.
TMP really is not an ensemble movie the way Trek should be. I read a recent review of TMP not that long ago that mourned how Spock supplanted Uhura. Uhura could have figured out how to communicate with V'Ger. Uhura also could have figured out the whale-song in Trek IV. After all, she's a communication's officer, right? Shouldn't she know how to do more than merely open and close communication? Shouldn't she know something about language and data encoding and things like that?
Same with Kirk. Kirk could have been given more opportunities to show his unique leadership abilities. He certainly "cheated death" in Trek II.
The novelization of TMP supposedly goes into more back-story on Kirk's subconscious anguish over not steering a Starship and how it made him kind of an A-hole. The novelization posits that McCoy quit starfleet when Kirk accepted promotion as an act of protest. Certainly Decker's dialogue points towards Kirk's dysfunctional personality, but there's more to it in the novelization that didn't get filmed.