* Magikarp is easily caught: Magikarp is a very common Pokémon with a low catch rate. However, it's still very easy to catch with regular Poké Balls, especially if you use berries and throw a good curveball.
* Master Balls are extremely rare: Master Balls are the rarest item in the game, and they're meant for catching extremely rare or powerful Pokémon. Wasting one on Magikarp is a huge waste of resources.
* Magikarp evolves into Gyarados: Magikarp is a stepping stone to the powerful Gyarados. While you might be tempted to skip the evolution process, Gyarados is much more valuable than Magikarp.
In short, using a Master Ball on Magikarp is like using a diamond to make a paperweight. It's a complete waste of a valuable resource.
Instead, use your Master Ball on a Legendary Pokémon or any other extremely difficult to catch Pokémon.