The tax income is dependent on the tax rate you set, higher rates reduce population happiness. You need to look in the details screen to see it rise, larger cities often appear less profitable as they pay more army upkeep costs.

To increase Farm income, either build upgrades (may be cause of regret later in game) or have Governors with good farming traits and priest retainers who improve harvests. Temples may be built to increase farm production, and later changed when population grown, and anti-corruption temples preferable.