Shore diving in rustic areas pretty much guarantees that the property owners/renters are encumbered in awkward gear, literally weighted down, wearing fins and can't run fast, and will reliably be gone out of sight over 45 minutes. They are likely tourists and will leave the island (probably the country) within a week or so. And law enforcement won't be going all 'C.S.I.' tracking down petty theft perp.s.
Put your rental truck key in some sort of dry box (some of us like the new
DryFob), leave your doors unlocked and windows down (as tursiops said, if not raining), don't leave anything of value except scuba tanks in the vehicle (or minor things you can write off it taken; sunglasses, flip flops, a 2-L plastic bottle of water frozen to provide drinking and rinse water). Don't leave camera gear, cell phones, money, etc...
That usually avoids the problem. In fact, if you do those things, and lock your apartment door, you probably won't have a problem.
Disclaimer: Once in awhile we hear of disturbing atypical violations, like when the spare tire was taken from the vehicle of your friend and his wife. Or a battery is stolen or gas siphoned. Those accounts seem few, but I would imagine could be highly aggravating. In a nutshell, not likely but of course I can't guarantee you anything, any more than I can do so regarding your own car back home.
We occasionally hear reports of burglaries of accommodations. It's been my subjective impression from forum reports that it seems more of those were in small or single residence accommodations, rather than on larger dive resort grounds like Buddy Dive Resort. I haven't rented condo.s and I'm not saying don't. I am saying if you have a higher than usual anxiety level about crime, a room on grounds in a big dive resort might help you feel more comfortable.
I've found Bonaire a pretty safe place to get out and walk around, even late. I don't go out looking for seedy looking places, drugs, hit on local women, get drunk in bars, etc... Most anywhere you can find trouble if you go looking.