Never automate workers in the early game. You need to have a clear improvement path planned out for every one of your cities, accounting for growth, production, happiness and expansion.
The only time you can afford to automate is when your cities are so well positioned that the effort spent on microing the workers further is no longer worth the number of clicks. Or during conquest, when you don't really need to setup each and every puppet city perfectly.
Remember, Civ is a game of compounding advantages. The smoother your start, the more benefits you'll reap over time, but once you hit the mid or late game, spending effort on things that don't have an immediate benefit isn't really worth the time at all (unless you're seriously min maxing).