With Tropius, it's a matter of how stupid it looks.
Ok, yea, he's a flying type. And yea, he can fly. But that's just a game mechanic and a bit of lore. When he's actually shown flying, it looks ridiculous and silly. He's a giant dinosaur.
Also no bird except hummingbirds can just hover/flap in place like that. Flying takes a lot of energy, and so most birds don't do it if they can help it, or "cheat" and use thermals or other tricks to reduce energy used. It's okay for a few flying types like Zubat or Fearow to remain in constant flight, as they're usually shown able to do so, but not 75% of flying types.
Much like Tropius, there's a lot of flying types that we just kind of pretend are flying types, in the back of ours minds and don't really think about how silly it would be for them to fly. You see a Tropius Sprite and you just think "he's Grass/Flying, okay" and your imagination just sort of fills in the blanks. So we don't need to be reminded front and center that these Pokemon fly when they clearly should not be able to.
Also quite a lot of these Pokemon were never designed for constant flight, and so they have details on their bodies you can't see well when flying. Like Xatu and Skarmory.