Hi, don't know if you'll still look at this thread after 6 months....
But my DS, who has just turned 4, developed a severe phobia of balloons at around 2 years old (from one banging). This has developed to a fear of the hoover, a fear of hand driers in toilets, and a fear of the noise of trains. (He also used to cry at muscic groups when the singing started!)
He does the same thing with his hands over his ears. There was a time when I was convinced he had over sensitive hearing, and I googled something like "loud noise children" and the first result was a site about the most common fears in children.
The most common fear for a 2-4 year old is loud noises. As children develop an awareness of the world, the most common fears change, so at some point I remember the most common fear is strangers.
So it might be that with your DS. But I do think children have better senses than us anyway (sensitive taste buds and better eye sight for example!) I remember there was a certain cafe my mum took me to as a child which I hated because the acoustics there made the knives and forks clatter so loudly!
I was actually looking for a chat on whether to take DS to cinema, I have been holding back because of the noise thing, but he really wants to see Bolt! Now I am thinking maybe wait a bit more if your DS has found it too loud.
Looking at my own message, I wonder if perhaps it would be better to have a check up and ask the Doc/Health Visitor about it. Let me know how it goes! x x