I'm actually very fascinated with the rank structure in Star Trek. When I watch episodes/movies, I am very aware of how many pips or stripes so-and-so is wearing, and who outranks whom. It is part of the fun of Trek for me. Some of my biggest gripes are the costuming errors prevalent on the shows by those with limited understanding of rank structure, such as Chief O'Brien having multiple ranks before officially becoming a Petty Officer, and Chakotay wearing Lt. Cmdr insignia despite being referred to as a commander. Tuvok wore Lt. Comdr insignia most of season 1 of Voyager before someone fixed the glitch, then they promoted him anyway later in the series.I don't know, I don't really have any desire to see a proper military Star Trek.
This movie was an abomination in the way rank was handled, but a lot of that can be hand-waved as the mistakes of the writers/costumers. They may have been unfamiliar with how rank actually works, and as others have stated in this thread the whole point was to end the movie with Kirk as Captain (a plot point with which I still disagree).
If you think about it from an outsider perspective (i.e., someone not part of the main cast), there are going to be a ton of officers who are pissed that Kirk rank-jumps them, especially since they've put the time and effort into becoming command division personnel. The lack of diplomatic experience is also a hindrance to Kirk being a successful leader. Also, the film generally shows him as hard-headed, and despite the fact that he does save Earth he probably should have been thrown in the brig. That kind of insubordination shouldn't be tolerated, let alone rewarded.