Originally Posted by
Augustusng
Check the regional effects and your empire maintenance. Each region has various effects that are displayed in the bottom left corner. Mouse over those to check. Some of your regions will have negative modifiers to your tax rate. Added to higher empire maintenance as you expand, it means some of your regions will produce 0 income, unless you increase the tax rate (either through buildings/traits, slaves, or the tax slider), or decrease empire maintenance (done mostly through character traits and technology).
Basically, all your various income modifiers (+% from agriculture, industry, commerce, etc) are added before accounting for tax rate, empire maintenance, and slavery. Those three add/subtract from each other to influence how much money you're actually making.