A chip is *supposed* to increase performance by changing the fuel/air mixture map and any other parameters stored in the ECU that the chip maker thinks will help. In the case of an automatic, they can also change the shift points. However, they're making one generic chip for all cars of a given specification (ie, year/transmission/engine size) which isn't much different from what the car manufacturer does. So on an average car, you may not see any performance increases at all. And depending on the mods you've made, you may actually HURT performance with a generic chip.
It can be argued that if the car manufacturer can get 95% of the best performance from a car, they're not going to spend lots of $$ to get that extra 5% while an aftermarket company might. Also, the OEM is concerned more with average fuel economy and best performance for the whole LINE of vehicles rather than an individual specific unit (although the chip makers have the same problem).
Regarding the fans, Hypertech had two units that I'm aware of - one was a CoolChip (IIRC) that worked in conjunction with their lower-temp thermostat to make the car run cooler (which increases performance) and the other didn't do anything with the fans. That second one is what's in my car.
The blanket statement I made, btw, is based on some reviews of chips that I read about last year while researching what to put in mine. If you do a Google search, you'll find them (I didn't keep the links). They essentially say, in more words, what I said above - a generic replacement chip, on average, won't do anything for you.
This pertains to NA cars, btw. With a turbocharger, controlling the boost by changing the ECU is a proven means for getting more performance at the cost of stressing the engine more.
[RICHR]
