This is going to be a long post....
Start with something that produces using only Energy Cells, something like a Wheat Farm in Home of Light or a Swamp Plant Factory in Greater Profit, these are the cheapest to maintain, since you can set the buying price for resources down to around 13-14Cr and sell for at least average price. Another good hint is that Herrons Nebula, north of Argon Prime, is the only place in Argon Space where you can legally build a Space Fuel Distillery, if you link that up to a Wheat Farm, and get a Transport buying Energy Cells, it can prove pretty profitable (but risky, mostly Space-Fuel sells in Pirate Stations, be prepared to lose the odd seller now and again).
The trick to automating a station is the Homebase setting in the ship control panel menu, always set your Transport ships up as well as possible, make sure they have the usual Trading System Extension, Navigation/Special Command Software, Fight/Trade Command Software 1 & 2, and Best Buys/Sells locators, a Jump-Drive helps greatly as well, but can be hard to get hold of outside the Argon Homeworlds, the Freighter
will usually be more expensive to buy than the Station it works for (and, in my opinion, don't have nearly the survivability/cost ratio they should have, but there you go).
Open up the control panel for the new freighter, and make sure everythings assigned properly, particularly make sure the Homebase setting is set to the station you intend the Freighter to work for and that any Jump Drive settings are assigned. One little personal note of experience here, look for the Mosquito Missile Defence plugin here
http://forum.egosoft.com/viewtopic.php?t=226431, load up with about 100 mosquitos and switch it on using the 'additional commands' list just under the standard list in the command console, remember to assign the mosquito to the freighters missile launchers. It adds a lot of survivability to the Freighter.
Once you've assigned your homebase, the Trade Options should have the Buy/Sell for Best Price option available, which allows you to order to the ship to perform simple buying or selling for the station, the ship will repeat the command until told to stop and will auto-drop the bought resources into the station. The Commodity Control software is more advanced, you need to assign which materials the Trader deals in, when to buy or sell, and where to buy or sell, it's probably best to get more to grips with how the whole market structure of the game works before tackling it, I'm still working on getting beyond the most basic use of it, to be honest

One final hint, one of the best ways to make money is to build goods that require Silicon and mining that Silicon yourself, if you get a Demeter Miner from Paranid Prime, or simply fit any TL with an Ore Collector and a Mineral Scanner, once you have assigned a homebase, there is an option in the Special Commands menu called 'Mine Minerals', you can tell the freighter where to mine, what to mine and where to deposit the minerals once it is full. The only down side is that it doesn't auto repeat. Find a nice Silicon Asteroid, blow it up, and get the miner to collect the pieces, it can save a fortune for things like Crystal Fabs or Chip Factories.