As a net-decker myself, there are a few reasons:
Variety — once you get closer to the top of the skill tier, you increasingly run into the same decks over and over. The moves will feel the same, the experience gets samey, etc. The less balanced a meta, the more a problem “netdecking” is in this respect because people will gravitate towards the dominant decks.
Player development — this is more an issue with younger players, they get into the game and want to compete and immediately go for the meta thing without understanding why the meta thing is good. This issue is less of a concern with seasoned players who want to compete without investing the time to scrub cards for synergies and potential.