"Why is crime on Bonaire so prevalent and accepted that you dare not even risk the chance of leaving something of value inside of a locked car?"
Short answer from other thread(s) is you're likely to find this issue in any area combining the following factors:
1.) Large numbers of shore divers, especially with rental vehicles, so locals know parked rentals by shore dives sites will be abandoned for around 45 minutes to an hour, & people returning will be in water & encumbered by gear, easily outran. Victims are mainly tourists who won't have local connections, or be around long enough to make prosecution likely in the highly unlikely event one is caught.
2.) Likely thieves in the area. Regional poverty seems to be a risk factor for that.
Richard.