In no way was I generalising my response to other people's babies who are scared of loud noises. I was responding directly to the OP
Whilst I hope that it is a simple case of becoming sensitive to noise as a developmental phase (that still isn't 'no reason', it is fear due to sensitivity to noise, not just to exercise lungs!), I was thinking that it may be a case of DP being a little insensitive to the bub and not realising the effect it could have on him.
Yes, bub will still love his daddy, and he can incorporate his fear of daddy's voice into that love. I know kids whose fathers love them dearly, and come from the 'old school' of 'smacking has its place', 'I turned out fine by being yelled at and smacked' (ummm, according to whom?) - their kids hide and run (VERY fast!) when they have done something they know they shouldn't have done...because they are scared of their beloved daddy's reaction. I love my mum, but I think that whenever she raises her arm to scratch her head I will forever draw away and cringe, from the time when I was young that I would cop a slap or whack for the smallest thing (she of the school of thought that to 'punish' the smallest thing would prevent bigger transgressions from happening...). I've accomodated that conditioning into my interactions with her.
I hope I'm way off and that Jonathan is just a sensitive baby who needs stimuli in his environment to be presented to him sensitively (certainly not eliminated or he might become a bit intolerant to change later on!). Otherwise, listen to your gut instincts