Bonnie has several delusions.
The reason why Bonnie appears to be the only human in the setting is that she is suffering from lycanthropic intermetamorphosis, a condition that causes her to see other people as animals. As such, Bonnie has no qualms about serving her neighbors to her customers because she is unable to see them as people. Her killing you can be interpreted as her thinking you're an animal that escaped from its cage instead of doing it out of fear of being exposed.Bonnie may also be suffering other delusions that cause her to view her world as sunshine and rainbows as evidenced by the first half of the game being two-dimensional versus the second half of the game.
Bonnie does what she does out of necessity.
If there are no non-sapient animals in her world, then Bonnie most likely has to source the meat she uses for her pastries from the people around her. There is another killer in town.
Bonnie became a monster simply because she disposed of a rabbit she tried to heal. One covered in wounds caused by someone else. The rabbit may have escaped someone who has been killing animals long before Bonnie did.- This seems to be confirmed in the DLC since children have disappeared but Bonnie wasn't responsible of it, which means that there is a second killer in town.
