Because the diseases that are easily killed by your immune system don’t spread, they get killed. The ones that have some mechanism that keeps them from being killed easily (usually multiple mechanisms, like stealth, or speed of reproduction, or ability to fight off the immune system) are the ones that survive and spread enough to actually succeed.
Imagine if you rolled a hundred objects of different sizes and shapes down a hill of grass. Your question is asking why the 5 that made it to the bottom weren’t stopped by all the grass. The answer is that the grass did stop 95 of them, these 5 are just the size/shape that enabled them to roll on anyways.
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