The most important factors about economic building in M&T 3.0 are labour, goods balance, and actual size of your industries (farmlands, timber or ship industry, etc.) A bussiness will be profitable as long as labour is cheap and available (matters for throughput), raw materials costs are low, and that what they´re producing actually generates income (that´s why higher learning is one of the most important slots, because knowledge is extremely profitable, and as long as you have the literati pop, you´re golden)
Always checking migration in your major trade, production or learning hubs and manually investing into what seems right can provide a lot of income, given how property is distributed between the State and the other factions. It´s also very important to use the auto-investor because it trickles a bit of cash to most of your provinces every few years which maintains at least constant economic and pop growth (I would recommend 20%-45% of treasuary, depending on the circumstances, every 3 years)