I saw the movie Watership Down for the first time a few months ago (right before Easter, which made all those cards with bunnies on them suddenly look very morbid). For anyone not familiar with the story, it's about a group of rabbits led by the brothers Hazel and Fiver who leave their old warren to start a new one and encounter several predators and enemies along the way. It's one of the darkest and most highly acclaimed children's movies ever made, and while I did love it, there's one nitpick about it that bugs me every time I watch it.
The most likely reason is because characters like Hazel, Blondie, Jack Burton, and James Bond are more serviceable to audiences than their sidekicks are. They have less distinct personalities, so it's easier for us to project ourselves onto them and pretend that we're the ones living their lives. This type of character is often referred to as a Blank Slate, and while they're still commonly used in storytelling for the above mentioned reason, we do see a shift in their role as the protagonist every now and then.
Just look at the Pirates of the Caribbean movies. At first they seem to present another case of a Blank Slate protagonist who's going to have a dynamic sidekick, but Will Turner quickly gets demoted to a helper after he meets Captain Jack Sparrow. The two spend the rest of the original Pirates trilogy pretty much competing with each other to be the main protagonist, then Will drops out of the series altogether in the fourth film and Jack has the stage to himself. It's almost like the screenwriters were afraid to make Jack the hero at first and gave him a more standard counterpart to be safe, then when they saw how popular he was with audiences, they took off his Will Turner training wheels and edged him into the leading role. Sources say that Will is supposed to return in the fifth Pirates film, though it's unclear whether or not Jack will have the same relationship with him as before.
Judging from these examples, audiences seem to like having more memorable main characters. The recent criticism of Twilight's Bella Swan and poor performance of Hardcore Henry, an action film shot entirely in the first-person point-of-view, also seem to suggest that a lot of readers and filmgoers want more than a Blank Slate to project themselves onto. So again, why are so many three-dimensional characters relegated to sidekicks and supports for one-dimensional ones?
Whatever the case, it's still nice to see a second banana grow ripe and get picked every once in a while -- or a second carrot, if Watership Down ever gets any sequels.