If you have declared a capital and have tax rate set, taxes are collected by colonies periodically, and some of the money is transmitted to your capitals once per day.
Income tax is collected for work done in cities by pressing the "Go" button on manufacturing consoles, research, etc.
Sales tax is collected based on cities' populations own sales activities, and by commodity sales (when goods are bought by players and ships, etc).
Subsidy tax is collected when goods are sold by a subsidized spaceship.
You need a capitol building to declare that colony to be the government or sector capital, and it has to be either the leader or vice leader character of the civ doing the declaring.
Without a capital, you cannot collect taxes in your empire at all.
Without a bank in a colony, that colony cannot collect taxes or hold any money.
The number of bank levels in a colony determine the maximum amount of money its bank can hold.
If you do not set a tax rate, you will not collect taxes in your empire.
12% income and sales tax rates cause no morale penalties or bonuses, and are generally considered ideal. Setting them to 100% is a good way to cause massive morale penalties in case you wanted to deliberately decay a colony.
You can set the subsidy tax higher than 12% without incurring any penalty besides making trade less efficient for trade ships' own profit margins (but taking away more of the profit for the cities they sell goods to).