As Mathemagician has said (and he stole my suggestions, you bugger!

), I'll repeat the following:
1) There are three automation options. General improvements, improve nearest city, and
build trade network. Put every third or fourth worker on "build trade network," and they'll rush to hook up all resources in your cultural borders, and when they don't have anything better to do, they'll cover every tile with roads and railroads. And, even better, they'll leave you to decide what to do with the other tiles.
2) Go into the Options screen, and select "Workers leave old improvements" (so your workers won't go around countermanding your orders) and "Workers don't touch forests" (Patch 1.52; so workers don't automatically cut down forests--if they build an improvement on a resource, that can chop down the forest, but that's the only time).
I REALLY wish there was an option to go into a (to be added) Governor Options screen for each city. Have a little triangle (like in Master of Orion 1), and you tell the governor how much percentage to focus on food, hammers, or commerce (and this tells workers what to emphasize), or something...
Oh well.
