Because it’s not remotely one of it’s best counters. Even if you dismiss its crud movesets, it takes neutral damage from both Thunder and HP and is weak to Blizzard. Why on earth would you be surprised Blizzard destroys a flying type?
Raikou is the superior option hands down. Grasses are more viable against it when it has Thunder or HP. Blizzard is his best defensive move and answers are harder to find when he has it.