You know what the worst part of most traditional stories is? The protagonist. Protagonists are never the best part of anything. This is why ensembles were invented. Protagonists are like... walls. They're functional, and you can decorate them a little bit, but it's the rare wall that really grabs your attention.
1) You know exactly what's going to happen to them
When it comes to protagonists, there's a lot that makes it really easy to not engage with their story. First of all, a lot of the time their development is basically just the hero's journey again. That's not to say that a story with the hero's journey can't be good. Any trope can be good. What it does mean is that the protagonist tends to have a path that is fairly predictable mapped out for them. Which tends to make them the least interesting person around.
Examples: Harry Potter, James Bond, Duke from G.I. Joe, Will Turner and Elizabeth Swan from Pirates of the Caribbean, Luke Skywalker from Star Wars, Neo from the Matrix
The one in the center, there. She was the least interesting one. (Image: Dollhouse, Fox)
2) They're usually bland and boring
Protagonists, because they're going to be the center of the marketing plan, also get all their edges filed way the hell down. And, in an effort to make them relatable, chances are they have had everything that makes a person interesting and dynamic turned into something bland and generic. Although we are, thankfully, finally seeing executives cling less to "likability" as a requirement for protagonists.
Protagonists also have to carry a lot of the plot on their shoulders. And that can be a huge problem if the plot is bad. A side character can still be fun and entertaining even if the actual story they're in is bad. The protagonist can't shed the weight of a bad story nearly as easily. If the show's going down, the protagonist is probably going down with it.
Examples: Will Turner from Pirates of the Caribbean, Jake Sully from Avatar, Frodo Baggins in Lord of the Rings, Raleigh Beckett in Pacific Rim, Barry Allen in The Flash, Echo on Dollhouse
3) The supporting characters are more interesting than they are
This goes part and parcel with protagonists being bland, of course.It is very rare that I come out of a movie or television show or movie thinking to myself, "Man, would I love to know more about the guy everyone spent the whole time talking about." But I have come out of a theatre demanding to know everything humanly possible about that character that was only in five minutes of the movie.
Supporting characters have all the benefits that the protagonist does not. There's a lot more open to interpretation because everything about them hasn't been spelled out. They can be weird, funny, crazy, interesting — all the things the protagonist usually can't be. And since they aren't locked on the hero's journey, it's a lot easier for the writers to make their storylines much more surprising.
Examples: Boba Fett, Agent Coulson in the Marvel movies, Agent Carter from Captain America: The First Avenger, Daryl Dixon in The Walking Dead, Wolverine in the X-Men comics, Methos from Highlander, Sierra and Victor from Dollhouse
Also? When breakout characters have been brought up from the minors to the majors, they can start to suck, too. Remember when Felicity Smoak was a beautiful and pure light? She's not awful now, per se, but she's definitely not the spotlight stealer she used to be. How about Helo from Battlestar Galactica? They didn't kill him like they planned, and then, by the end of the show, we had Helo doing whatever plot-convenient job they could find for him that week. When characters are around sporadically they're mysterious and interesting, but too often the more you know about them the more you realise there's not much else to them.
Examples: Agent Coulson in Agents of SHIELD, Felicity from Arrow, Amanda from Highlander, Spike from Buffy, HRG from Heroes
4) They're very rarely diverse
Protagonists, especially in movies and television, almost always default to white male. It's an endless sea of white men all going on the same journey. Joseph Campbell got a few things wrong in with the title "The Hero with a Thousand Faces." There's way more than a thousand of these dudes running around. And they don't have a thousand faces — there's pretty much just the one. (Although the hair can come in blond or brunet.)
Examples: PRETTY MUCH EVERYBODY