This is a fun game. Well done.
Here's some feedback that might prove useful.
1. A simple page of help would go along way as I also tripped up on the need to click on fields to harvest food. I also completely overlooked the dock system for adding resources.
2. A button (ESC perhaps) to free up your mouse pointer from the build menu. If I've selected to build a house and I then click on a bunch of fields and orchards to harvest food then I find myself occassionally inadvertently building more houses when I misclick on the wrong square. Being able to hit ESC, or something else, and quickly deselect to a straight mouse pointer would avoid this.
3. Couldn't figure out any game effect for happiness or rain. I ignored both as a result.
4. Towers appeared to be bugged. Build one and two workers are deducted but very soon after they return.
5. The strategy of systematically ringing your island with Towers as early on as possible kind of made the pirates a bit pointless and devolved the game into a straight build up the resource engine until you've got enough to win. Without a full set of towers the game was really good fun and forced some tough decisions on you. Not sure what the answer is here but an 'easy-to-implement' game tweak that kept the Player in the tense, decision heavy, pirate environment would go a long way.
6. The game options to vary the speeds are much appreciated.
I think you've got the elements of a winning game here. Find a way to generate some variety and maintain the tension and it could be something that can be developed into a commerical product.