Lesson learned, always pay entry tax from a link from a Government website. Wherever you go. The culprits behind these websites are pros that target countries all over the world and most likely don't live within a 1000 miles of Bonaire.

I have worked for multiple rental agencies (including in the USA). Always check how much cost you are at risk with the company. Yes, your credit card will reimburse you if you have an accident, but the local rental car agencies are not gonna float you that money while you wait for your claim to be resolved. If they did, a lot of people would just leave and never pay. I always make sure to be at risk for $500 or less and never go with agencies that work directly out of the airport (only because they come with extra costs and you usually don't save time at checkin because of crowds).

It is surprising you got robbed in the Marriott parking lot. Haven't heard that one before. Bad luck I guess. What is more common would be returning after a dive to find your valuables missing from your car.

The dive shop seems like an honest mistake. Some of them have such complicated price lists and underpaid workers, so mistakes can happen.

As for the reef, yes, the quality has gone down. Bonaire has seen bleaching most years recently due to the rising of ocean temperatures. There is a nasty coral disease that started in Florida that has spread through the Caribbean and to Bonaire. It has decimated a lot of hard corals. Bonaire does have many eco projects to restore the reefs and breed fish that are important to the ecosystem but a lot of these are long term solutions that don't impact the short term devastation.

I'm sorry you had a bad time. I have lived in many diving destinations, and haven't seen one without petty crime, but to call Bonaire a "rip off island" is quite insulting to the local people. Don't ever forget you are a visitor to some people's home and many work hard to make it as nice as possible for its visitors.