That's kind of the whole point of his character. The Incredibles is a deconstruction of the superhero genre that questions what makes someone a superhero in the first place and if they really would be needed if they did exist. The suicide save at the beginning where he cripples the guy while saving his life is pretty much the perfect example. It seems obvious that saving someone trying to kill themselves is a net "good," but he took someone miserable enough to be a victim of suicide and then permanently crippled them. That's unbelievably fucked. That's the "survived suicide attempt but life is even worse" nightmare scenario that normally results in repeat attempts. Syndrome is a sympathetic villain in the sense that he has a completely understandable gripe with society and superheroes in society. He recognizes the ills that when you give people immense power, they can do damage even when trying their best to solve it. On top of that he has personal reason to distrust their role as an "elite" class, while it's somewhat of a childish grudge from his perspective he witnessed it firsthand that they instinctively distrust and view non-supers as lesser.

The thing that makes him a villain is that he recognizes the ill but fails to recognize the cause. The cause is not the questionable role of power and the oversight of it, it's the individuals weilding the power. If he just systematically eliminates them as a class both via outright murder and eliminating their uniqueness via uplifting the remaining the population, the problem is solved. There is no issue with the power, the problem is those weilding it are an elite class.