This. Obviously the thiefs in Bonaire have learned how to take advantage of opportunities. In Vancouver theft from vehicles is relatively minuscule, but go to any walk-in-campsite in the surrounding area (and there are hundreds) and you will see signs plastered all over the parking lot advising against leaving any valuables in your car and suggesting to leave your doors unlocked. The parking lots are often completely surrounded by trees, a few miles from any town and a few hundred feet from the actual campsites. Generally, campers have expensive gear and will leave SOMETHING in their car. This all adds up to it being the perfect robbery opportunity and the local low-lifes know that. However, it doesn't deter me from going camping where I want to go camping.
I don't really find it that weird that the rental car companies in Bonaire have told people to leave their doors unlocked as a result of high theft rates. I would be thankful for the suggestion. I've stayed at many accommodations in my life (from hostels to 5 star hotels) that will make you sign a waiver along the lines of "...any damage to drywall or furniture will result in a penalty of [insert ridiculous amount of money]." They're simply reacting to multiple bad situations in the past.
Obviously I understand the logic behind leaving your car door unlocked, but I don't think it's a good idea in most situations. If I left a $20 bill on my dash, I would think someone may try the door and if it's locked, their thought process would be to carry on. I doubt that most people would take it to the next level and smash the window. But, as Lorenzoid pointed out, places like Bonaire are a rare situation, where there's likely no one around to hear someone going through the window...