I'm a paediatrician. I've started about fifty billion (well that's an exaggeration, but lots) of babies on antibiotics. Sounds like you haven't had great communication, which is rubbish.
Basically, when a baby has an infection, it can move really fast and be really dangerous. Thankfully infections in babies are rare, but we have no way of knowing which baby will be affected. However, early antibiotics are really effective at stopping it in its tracks. So, we get to the point of who do we treat to make sure we prevent as many life threatening infections as possible. The answer is we treat ALOT of babies. The great majority never needed them in the first place, but for some babues, this will be absolutely life saving. So we treat alot, in an attempt to miss as few as possible. Nice guidelines say that if you have a couple of risk factors (gbs, mum having a temp, your waters breaking for a little while and a few more) or if the baby shows any symptoms (basically does anything strange) the safest thing is to give antibiotics. When you are inserting the cannula for the antibiotics you send off about 1ml of blood for culture. This means you put the blood in a petri dish and see if you grow anything. Unfortunately, things take time to grow so it takes 48-72 hours to determine that nothing will grow. At the same time you send some blood for infection markers (which come back in a couple of hours) . You send another sample off at 24-48 hours to recheck infection markers. If either of the infection makes or the blood culture are positive, your baby needed the antibiotics and they are continued if not they are stopped and you go home.
The antibiotics we have used are pretty old school and so have been used on countless babies and are generally very well tolerated. You are somewhat right that some studies have shown very minute increases in atopy in babies given antibiotics. However, this is a small effect and may even be explained by the fact that premature babies almost always get antibiotics. Overall, this is a really low risk intervention. My personal opinion is the cannula is the worst bit of it. A rip roaring neonatal sepsis is a million times worse and can have awful outcomes. So weighing it up antibiotics are a sensible choice for most. I really believe you have done the right thing. It won't wipe out all his flora, but if you breast feed for a little bit that will really help with that as well.
Also my 11 year old had antibiotics for two days at birth and is as healthy as an ox. My 9 year old didn't, and had asthma!
Hope you feel better. The post natal wards suck, especially at the moment, and learning you've got to stay another couple of days is soul destroying, but it will be over before you know it. Good luck.