If your child has - a fear of noises from the toilet:
Show them the workings of the toilet to take away any fears they may have relating to where the water comes from/goes to, how the flush mechanism works and what it is that makes the noise when the handle is flushed.
Put food colouring in the cistern for them to watch when the toilet is flushed to distract from the noise.
Store a couple of folded bath towels on top of the cistern to dull the noise of the cistern being flushed.
Encourage your child to put the lid down to reduce flushing noise.