All of my (3) children are afraid of toilets - they are 5,4 & 2 ---- especially the automatic ones. I struggle with it. What I have found works best is to say (in a happy sing-songy voice) "oh come on - there is noting to be afraid of" all the while making sure that I try to stop the auto flush. If it happens - I agree with them - "yes, that IS scary and loud"... For some reason, with my kids just having their concerns validated seems to help. It doesn't make the fear go away - but easier to deal with. So, every trip to the restroom has to start with me being at my highest "great mom" state - full of fun and energy.
I know - sounds like a pain and may not work for yours - but,I promise, it works for mine.