Why is 100 volts or less generally "low voltage" and "safe"?
There are undoubtedly various points in the past when different thresholds were set for classifying voltages in terms of safety, but I don't think this is what you are asking.

Different standards employ different thresholds. For example, so-called "extra low voltage" is defined as under 50VRMS AC or 120VDC (see https://en.wikipedia.org/wiki/Extra-low_voltage). We can say that in general, the voltage range between 50 and 100V is where it becomes more than infinitesimally likely that the voltage could induce enough current through a human body to injure it. 

It would indeed be absurd to claim that any voltage at or above a certain threshold will injure or kill, while anything one volt below is unconditionally safe. Individual people and the circumstances under which they encounter the voltages in question introduce plenty of variability into real-world situations.

The point of setting a limit at 100V, at 50VRMS, or at 120VDC is not to claim that there is a sharp line of demarcation in terms of the actual effects. It is simply a matter that whenever you make a standard, you have to draw a somewhat arbitrary line somewhere.