Buildings were compensated directly into wallet (reals), compensation for shipyard (doubloons) was provided via the redeemable box (if you had it)
@Gregory RainsboroughYou can sell tobacco with profit in national Capitals. Regarding the rest - you can still earn good amount of reals compared to cost of a ship in resources. As this is Early Access, the numbers are not final, but the current numbers seems ok (more time and testing required).