I always manually control my workers until i develop railroads, then I automate because the first thing they will do is convert all roads to railroads, and by about that time i'm discovering aluminum and oil anyway, and they'll automatically track them down and harvest them.
I'm the same way. I never automate if it's on a jungle map though, because they just love to clear cut everything for a farm.
I'm in awe of those of you who never automate. When I have more than ~5 core cities and just as many puppets, I'll focus on my key 4 cities.
Once I'm happy with where they're at, I set them to automate and intervene on occasion.