We've all been there before. You're daydreaming, thinking of that next big book and the awesome protagonist you're going to wow your readers with, and you think - "man, what would really get some drama?" Then you clap your hands together, point one finger in the air and go: "Eureka! Orphan!"
I can't blame you, or me, for thinking that way. Making your protagonist an orphan gives you a lot of things for free. You get some drama (MY PARENTS ARE DEAAAADDDDD) free agency (nobody to tell you what to do!) and the classic (but difficult to use because: Star Wars) dramatic return of dead parents!
Plus, lots of dream sequences with your character going "no! no!" as their dead parents tell them how disappointed they are, or the MC watches them get killed over and over. All good! Additionally, it allows you to have extra characters and different tensions: Step-parents or foster families, or in the case of Kvothe, random homeless thugs and crazy people who take care of orphans. Your character doesn't have to answer to anyone, and they get to ignore a lot of the common rules that affect kids of that age (if your orphan is a kid, otherwise it's just a bit of backstory)
There's another reason authors choose orphans: It's easy. You don't need to write parents or siblings or home-town rivalries or whatever. It's just your protagonist, and that dark past they carry with them.
But what are you losing? What are the cons of making your protagonist an orphan?
Well, for one, it's predictable. When you have an orphan character, you automatically have these tropes that people expect to see. There are people out there (not many, but they exist) who will actually just put down a novel once they see that the protagonist is an orphan. One of the panelists at ConFusion was like that - he said he managed to tolerate Name of the Wind for doing so.
Tolerated. Because it's Name of the godzilla-damned Wind. Wow. But let's look at why he said that, and why he was able to tolerate, and really probably actually like Name of the Wind. He said he doesn't like orphan MC books because the same emotional traumas are present in every single book. The arc of self-discovery is the same. The tropes with parents and poor relationships with authority figures.
Why was he able to like NotW? Because Rothfuss dealt away with a lot of those tropes. He didn't focus on the character moaning about his parents being gone, instead he focused on what Kvothe was doing at that moment to survive. It wasn't about a lot of existential angst, or using dead parents as props, but about the repercussions of actually being orphaned at a young age. There was rummaging for scraps, getting the crap beaten out of him, learning to live on the streets. Those are things you want in the foreground, not in backstory exposition.
Additionally, he makes up for the loss in family dynamics with new parental figures. The teachers at his school, the friends he makes, the mentors he finds throughout the world. But you could have parents in addition to these and you wouldn't lose any value to the replacements.
So how can you make your orphans more interesting? The panel I went to didn't have a lot of suggestions honestly. Most of the writers there had been invited because they wrote novels with orphan protagonists. They suggested just reading other orphan based books and seeing what they did and just doing something different.
But I have one for you - don't let your character be orphaned. Have your character orphan themselves. Make them an agent in the orphaning process, not a bystander. Make that part of their character more meaningful than just "I saw my parents killed/I didn't see my parents killed." Maybe your MC did it on purpse! Maybe it was an accident and they feel terribly guilty. Maybe they were forced to kill their own parents?!?!
Ultimately, the choice of making your protagonist an orphan is up to you. But it's an important decision to make. Look at what you're gaining from writing an orphan, and what you're losing. Decide what's best for you and for your story.
And don't worry - the panelist who said he would never read another orphan book also said this: "Don't listen to me. Don't worry about me. Write your book, and if you're passionate, it will do well. Don't stop because of a single person's pet peeve."
It all comes down to the passion you have for your work - if your story goes one way in your head, that's the best way to write it. Don't force something that isn't there. If your MC is an orphan, they're an orphan.