We don’t necessarily, it depends on the extent and type of bacteria causing the mould, your personal susceptibility to that bacteria, and indeed how your body handles exposure – such as digestion.
It is a bit of a misconception that mould is bad in absolute, but for the ease of removing obvious mould from food – such as cutting the mouldy bit off some generally un mouldy cheese – you may as well do it.
Some of them can survive, but yeah, a lot of them do die in your stomach acid.
Buuut, there isn’t just mold/bacteria on the food. There’s also their poop which can be pretty toxic. Not to mention, some microorganisms seem to create some nasty toxins more or less intentionally, either as a normal part of their life cycle, or as a method of self defense. For example, the bacterium Clostridium botulinum produces an incredibly potent toxin that causes the sickness “botulism”.
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