While I haven't played the multiplayer in Destiny, I can say that I've heard people complain about shotguns in many, many games. The reason being is that nobody likes to be killed in one shot. They want a chance to retaliate, and if you die in one shot, you can't. It can be frustrating while you're in a groove to run around a corner and instantly die. I get it.
But shotguns are not unfair, just like sniper rifles aren't unfair. They kill people in one shot with the trade-off of being absolutely useless except in their ideal scenarios. The reason you use an assault rifle, for example, is because it's a jack-of-all-trades/master-of-none sort of deal. It's GOOD for just about any situation, but it's bested by weapons that are designed for specific situations. Wouldn't it be unfair if an assault rifle was better at close range than a shotgun while still retaining its range and fire rate?
If someone is good at staying in close range and picking people off with a shotgun as they run by, then that's how he or she should be playing the game. If everyone was running around with the same basic assault rifle, it would be super boring and tactics would never change.
Edited for typos.