As a general principle, one (we) need to be very careful to not disparge minhagim. Throwing aravos on top of the aron kodesh is a widespread practice, so it should stand to reason that there is a basis for it that has stood the test of time.
My Rosh HaYeshiva was fond of saying that “sevaros are a dime a dozen,” but I’ll conjecture why the hoshanos might be tossed atop the aron kodesh, but not the lulav: once the hoshanos bundle has been beaten, the practice is that no-one else uses it – that’s why many bochurim purchase an extra set for their “Alter-Bubbe” (I know I did when I was a kid). So, once you’ve “spent” the hoshanos in shul, there’s no reason to take it home since there is nothing left to do with it. By contrast, the lulav and esrog can be used throughout the day until Shemini Atzeres, and in fact those who are accustomed to eating an esrog should not do so on Hoshanna Rabbah since it maintains its kedushadiche usefulness throughout the day.