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I wish people would stop citing depictions of fairies taming and controlling insects as the end-all be-all argument, when realistically speaking the exact opposite scenario is literally almost as common.
It depends entirely on the work of fiction whether fairies dominate insects, or whether fairies live in fear of them. Pokémon is free to pick which one it subscribes to—both are perfectly reasonable.
They should not have sided with excuse that makes a weak Type even worse. And silly though it may be, yes it is basically true that Fairy Type is basically emblematic of little girls, and they're horrified of icky things like insects. Fairy Types are prudish and have high disgust sensitivity.