The point is, nerfing his Q hurts significantly more then buffing his combos, A LOT MORE. Base damages hurt a lot (See -3 ad base nerf on vayne, almost fell completely out of the meta after)
He uses his Q for everything and no 5/10/25 damage is a lot in the early game, when you have such low base health that can be the difference between someone dying and not dying. That base damage also affects how much your combos do, how much you can harass, push without your w, etc.
Your not keeping in mind in the fact that we are dealing with %, so late game it "Does more damage" but its still the same percent and as late game scales will have the same affect it had early on just a bit slightly more due to how things scale.
Zed wasn't in need of nerfs, he doesn't have a 49% win rate because everyone plays him, he has that because he is average, the average person who plays a game with Zed has 62 games on him. Thats more then enough to be at least decently experienced, so you'd think higher win rate right? Wrong, he isn't in need of nerfs, and the only reason he's getting them is because people dislike like him.