Transferring is also useful to drop cargo at stations which don't normally accept it. Imagine you have an oil platform, a dock nearby connected to a train station (you do that by pressing shift key while placing the stations), and a refinery far inland. Since there's no refinery next to the dock, it won't take oil; however, if you order your boats to transfer their cargo to the docks, you can then pick it up with trains and take it to the refinery.
When you blow up buildings and trees and terraform you piss off nearby towns. When a town is too mad at you, it won't let you build stuff near it. This usually happens a lot when building big stations, such as an airport. If you had some sort of transporting service at the city picking up passengers or mail you'll eventually gain their trust back, so it's advisable to set up a bus network in cities you're planning to expand to. Then if you piss them off you just have to wait a bit before you can continue building. Another trick to sooth angry towns is to plant trees near them.
Finally, the amount of stuff that primary industries produce is proportional to the ratings of the station you're using to pick up stuff from them. You can increase station ratings by increasing the frequency of cargo pickup. The more you have cargo sitting at a station doing nothing, the lower your rating. Industries themselves can also change production over time. These changes are random, but they will increase the most on average over time if you keep your monthly station rating above 80%. There is normally one exception to this rule found in Oil Wells in the Temperate climate, which can only ever decrease production until they dry up and close down.