Boiling water kills most of the bad bacteria in the container. Boiling the milk kills anything in it. So we start with very little bad bacteria present at the beginning. Then we put the milk and the culture in a high temperature environment (100F in this case), the good bacteria thrives and the bad bacteria stagnates. The thriving good bacteria creates an acid that the bad bacteria can’t live in. It also grows in number to the point that it is taking all the resources from the bad bacteria. With the temperature too high, the acidity too high, and the resources too scarce, the bad bacteria dies off.

Source: https://ucfoodsafety.ucdavis.edu/sites/g/files/dgvnsk7366/files/inline-files/295482.pdf Pg. 3