Regarding moldy food, it's because you're taking a gamble on what exactly the mold is. There's many types of mold, and some can produce very toxic compounds. Eating the mold can poison yourself. Of course, if you know that it's a safe mold, then you can eat it (that's how cheese making works). But as with all things in microbiology, things tend to be complicated very quickly, and it can be pretty hard for amateurs and even professional microbiologists to accurately distinguish between safe and unsafe molds.

With regards to killing helpful bacteria, you are correct that one of their uses is that they help improve the efficiency of digestion. This is a very young and growing field (and also not entirely in my field of expertise), so many things I say might be outdated. The second most obvious downside to killing helpful bacteria is that they prevent actual harmful bacteria from growing out of control. There are several bacteria (in particular, C. dificile) where taking antibiotics actually makes the infection worse, since the antibiotics kills off the helpful bacteria that were helping to contain the infection.

Scientists also have found semi-recently that bacteria in your intestines have an incredible amount of control over you as a person. Your body even has a sort of hotline that connects from your intestines directly to your brain, called the vagus nerve, and the bacteria in your intestines use this to communicate with your brain. For instance, scientists have found that the type of bacteria in your gut can influence the onset and severity of autism symptoms. One current hypothesis for autism is that the body, during development, somehow messes up the composition of bacteria in your intestines, and that in turn messes up the development of the brain. I seem to recall reading papers that linked bacteria to other neurological diseases and disorders, but I don't remember completely.

Another is that the bacteria are known to be linked to obesity. Scientists have found that if you give 2 people the exact same foods in the exact same amounts, one can develop obesity and one won't. Whether someone develops obesity or not is highly predictable based on the composition of the bacteria in their intestines. As a matter of fact, scientists have even found that if you replace an obese person's bacteria with bacteria taken from a healthy person, then the obese person will begin to lose weight, even if that person hasn't changed anything else.

The bacteria in your intestines are also known to be in constant communication with your immune system. I believe the immune system uses the bacteria in your intestines to train when you're young. But this back-and-forth extends well into adulthood. Scientists found that bacteria can control the development and activity of white blood cells. That, of course, leads to differences in things like fighting off infections and killing cancers.

The bacteria in your intestines are incredibly important, and we're only just now beginning to understand what they do for us. That's why I say that you have to weigh pros and cons. If you think you'd be fine without it, I recommend not taking antibiotics. But if the infection is severe, then it's worth dealing with the downsides. Talk to your doctor if you're unsure - he probably knows more about what situations are severe and which aren't. But what you definitely don't want to do (which I know many people tend to do) is to pressure the doctor into prescribing antibiotics. Antibiotics aren't a wonder drug, and people shouldn't be immediately jumping to antibiotics as a solution to their infections

I am not a Microbial Pathogensist, so I'll just use the internet's preferred method of saying something confidently that is probably wrong on some pedantic level and having actual experts climb out of the woodwork to correct me, but...

Mold isn't a single organism, it's actually a colony of many individual microbes that work together, most of the time; there are exceptions since the word "mold" is a lay term as much as it's a scientific term, and the common usage doesn't have the same rigor applied ("if it's slimy/fuzzy, it's mold" kinda reasoning).

The colony aspect is important, because you're probably inhaling mold spores and eating tiny amounts of mold every day. The microbial aspect means that eating a whole colony has the potential to infect you even if your body kills off 99.9% of the microbes.

As to why an infection is dangerous depends on the type of mold. Some take up resisdence in specific organs and starve the organ cells of vital nutrients, others are carnivorous and eat your tissues/cells, others may eat beneficial bacteria or starve them of vital nutrients, some secrete toxins that are relatively harmless in small doses but deadly with a full-blown infection—penicillin is a great well-known example of this: it's the chemical the mold uses to kill off bacteria competing for the same resources—, sometimes it's just the immune system's response that's dangerous.

If you want an example of what such an infection does on our scale, look up everyone psychonaut's favorite: Ergotism. The Ergot fungus grows primarily on cereals/grains and secretes chemicals that are psychoactive in humans (one of which is the precursor that Dr. Albert Hoffmann first derived LSD from). Unfortunately besides mind expanding insights into the nature of reality, it also comes with a nasty infection that can cause convulsions, painful burning/tingling/freezing sensations, diarrhea, vomiting, gangrene, psychosis, and more.

That all being said, if you accidentally swallow a bite of moldy bread, you probably don't need to freak out and call poison control/EMS; just don't regularly eat moldy food and expect to have your immune system stave off a full-blown infection for long.

why it’s bad to eat moldy food

For starters, it's poisonous and tastes like shit.