Those points are all valid, and the do pose a threat to individuals, though not to the existence of the human species. Evidence that we are still here, and in great abundance, more or less proofs that.
Pathogens have wiped out a significant portion of the human population, with something like the black death killing between a quarter and a half of all humans in the 14th century.
This was obviously before we even knew of bacteria, and certainly had no antibiotics or anything useful to fight against it, but some people were either immune to it, evade infection or both.
It's always a matter of averages: afaik we have not evolved any mechanism to protect us when struck by lightning. Surely some people get struck by lightning every year, and most of them do not survive it, the number is so small it doesn't have a significant effect on total population. If for some reason we lived on a world where people got struck by lightning once a year on average or so, we'd probably have evolved lightning rods of sorts... a bit like how electric eels manage not to electrocute themselves