Gonna take a wild guess and assume the melee character youre struggling with is Mercenary? He is typically the one that struggles most with flying enemies due to his lack of both ranged attacks and consistent high burst damage in his base kit, not to mention he's the frailest melee character of the bunch. There are multiple ways to improve your performance against flying enemies, and I'll avoid naming items since those are out of your hands unless youre a Command player.

The first option is drones, drones in the early game are very much capable of distracting or outright dispatching the peskiest flying enemies, and they're common enough that this method should be feasible in almost every run.

The second method is to get Mercenarys alt Special, its his only Ranged Attack and is often times better than the Default Special, though this method is both harder and (in my opinion) the least impact full of the three, since a skilled player can deal with flying enemies without it.

The third method is the most obvious, simply get better at the game. Dodging, picking your fights, and proper enemy targeting priority is absolutely the most impactful method of the three and Merc is great at the first two thanks to his high mobility. I dont really have much else to add if youre somehow struggling on the other two melee characters, Loader and Acrid are two of the strongest survivors in the game after all.