Auto repair prices are going to be different depending on which type of auto repair shop you take your car to. I've had a lot of experience with all of them and I'll help you figure out which is the best for your situation.
Car dealerships are repair shops that are set up to work on only one brand of car. Many times they know more about your specific type of car than either of the other two kinds of repair shops, but not always.
Many people think that they can only take their car to the dealership. This is not true and sometimes you are better off not taking it there. It just depends on how good your dealership is. While they can sometimes provide services that most other shops can't (reprogramming computers, etc.) they are also almost always a lot more expensive, in fact many people call them "stealerships"!
Since car dealerships are larger in scale, you will probably not be able to talk to the actual mechanic that works on your vehicle. If you have a dealership that does great work and treats you right, then you should continue to take your car there.
This is where the majority of auto repair shops fit. Independent repair shops are smaller, more personal and cater to individuals better. You can usually talk with the person that is in working on your car and many times you will deal with this person directly the whole time your vehicle is there.
The main downside to this type of repair facility is that the technicians are less likely to be trained to work on your specific vehicle make and model. Sometimes the equipment and tools in smaller shops may be insufficient for complicated repairs.
My opinion is that finding a good independent repair shop is your best choice. Sometimes they are even better than the dealerships at diagnosing problems with your car. They are also almost always quite a bit cheaper than dealerships.
The main upside to this type of repair shop is that their prices will probably be the lowest of the three types. They usually do very well at general repairs like brakes and exhaust work, but sometimes do not do as well with larger jobs and diagnosis.
While you will probably get a low price at one of these stores, there is a much better chance that they will try to sell you things you don't need. Mechanics at this type of repair shop are often only trained to work on certain vehicle parts. While good dealerships and independent repair shops almost always have ASE certified and factory certified mechanics, many times the chain type stores do not.
The most important thing to remember is to find a good, fair, honest repair shop and then reward them with your business and loyalty. This will be good for you both.