Blowing up all of the various bits of infrastructure around the island in Just Cause 2 doesn't cause the citizens as a whole to start rioting or rebelling. However, it does help the groups that are fighting it. Duh, people are joining one of the three factions against the dictator rather than fighting on their own!
The secret resource of Panau is oil which isn't so much a spoiler because the island is littered with pipelines, fuel depots, and gas stations.
Why is there a ship in the middle of a desert? Because the desert is actually a recently dried up ocean bed, like the Aral sea. The proof? "Lautan Lama" means "Formerly a sea" in Indonesian.
Rico's very own name has a nice meaning for the context of the story. Rico as a word in Spanish means "rich", which makes sense for him as his profession of being an Agent for the CIA means that he is paid handsomely for his work. Rico as a name means, "strong" or "hardy", Rico is a very strong soldier and is quite hardy or durable in the face of the all the danger he faces on a regular basis. Rico can some times be a derivative of the name Ricardo which means, "Powerful leader". Rico works for the United States which is in fact a powerful country, a "powerful leader", with a great deal of influence in global politics, and also acts as a (very effective) leader for various groups of gang members in the takeover missions.
In one cutscene, Rico says "Considering the value of the Panauan buck, shooting you would have been more expensive." What's one of the most common and convenient ways to refill ammo on your guns? Just ordering another gun from the Black Market and refilling your ammo off of that.
You have to destroy government infrastructure in order to destabilize the country. In addition, you receive no real negative feedback for killing civilians (unlike, say, Mercenaries). Why are you doing this? Because the new leader (admittedly a pretty nasty fellow) didn't want to dance to the United States' tune. Yes, you are basically committing state terrorism.
To be fair, he makes Saddam look like a cute cuddly kitten of peace and happiness.
Get a good look at the factions' territories and the way they're spread across the island. Panau is going to be a hotbed of violent infighting between them long after Baby Panay's been deposed and the oil fields nuked.