I'm sorry to hear you're going through this, especially as a first time mom. (((hugs)))
I know it's hard not to, but try not to worry about what others are thinking about his intactness. It's possible that even if he had been cut, he would have gotten an infection.
You asked why this happens. I've been reading about what makes us healthy for about 10 years now, spurred by my oldest's dairy allergy that I discovered when she was 18 months old. She had the allergy her whole life, but I didn't recognize it as such until then. There is a lot of buzz these days about our microbiota. I'm convinced that much of what we see in intact care "issues," (redness, inflammation, infection, etc.) when retraction isn't to blame, particularly repeated retraction, it's due to lack of normal, healthy flora. We're supposed to be covered both inside & out w/ bacteria & other organisms & when we don't have the right stuff, problems crop up.
You didn't say how he's fed. That effects things. How he was born. That too. What you were fed as a baby, how you were born, what you've eaten through your life, etc. It all matters. This is not to say that there's no hope, it's just that each thing has an impact.
If you are able, you might want to seek out an alternative care provider who can help you to make sure his microbiota is healthy. IF you're nursing and/or expect more children, you might want to see about it for yourself as well.
Best wishes & what a lucky boy you have! Congrats on him & leaving him w/ his whole body!