Remember that levitate can be used on an enemy as well. If they fail their save they are suspended in midair and a sitting duck. The flexibility to use on yourself, an ally or against an opponent leads me to think the current black rating is correct. It is a versatile spell. Also when the spell ends or you lose concentration the target floats down instead of falling like with fly. That is important if you are levitating and something bad happens.
But I agree that fly is better. That is why it's blue.