From what I've read so far it looks relatively straight forward to design and build a controller (a little knowledge can be a dangerous thing in the wrong hands). So what Am I missing? What makes them so expensive?
I'm far from the most qualified to answer this, but in a word: amps.
Assuming you're talking about controlling a motor for a car, you're talking about switching at least a couple hundred amps thousands of times/second. Many systems are switching 500 or more amps.
When you just want to switch a few amps, some fifty-cent mosfets will do the job. To switch the kind of current drawn by motors in cars, you need a device called an IGBT (a type of transistor). These cost more than a hundred bucks apiece and you probably would need several. On top of this, when you switch a motor on and off you generate voltage spikes which have to be "absorbed" and large diodes are used for this--these are not fifty cent items, either.
All this current creates a lot of heat which means heatsinks which means some fancy way of attaching the IGBTs (and maybe the diodes) to some serious heat sink material. One of the Zilla controllers is water cooled, just to give you some idea of what we're talking about here.
Then there's the parts to drive the IGBTs--these are not like "logic level" mosfets that can be driven with a micro--you need quite a bit of current to switch them, so now you're talking about driver circuitry (and components) for the IGBTs.
And, of course, you have to connect this all together--you're not going to do it with solder and one-ounce copper-clad PCBs
Those connections have to withstand the current, the heat, be low resistance, be reliable, and mechanically strong because you're attaching some mighty big cables to those IGBTs. Take a look at the inside of a household breaker panel to get some idea of what's required and remember that those are typically designed for 200 amps (open one up in the hardware store).
Then you have to package the whole thing up for the "hostile" environment it's going to run in: wet, cold, dust, heat.
And the list goes on....not simple, not cheap, but doable. Again, I'm talking about controllers for cars--things that draw less current are easier. If you're really interested, you could subscribe to the evtech mailing list at www.evtech.org. There's a guy on that list that's going through the process of designing/building one now.