Well this is a question that probably everyone that has bought a guitar has thought about. Let me ask this. Have you ever gone to a department store to shop and then find out that the item is cheaper or that there is a better selection either online or in another store? Sure you have. Guitar Center is set up to provide a wide variety of instruments and they command a large portion of the guitar economy. They get buyers, lookers and curious Georges. They don't expect to make a sale each time. It is the saleperson's job to sell merchandise. They know that most people will not buy from them but they do get many that do over time.
You should go to a place where you can find the largest selection of instruments to try out. If you like the price of the instrument and the salesperson and the store in general, buy it there. If you think you can do better some where else, then do so. No hard feelings are brought upon GC. They won't chase you down in the street. This is the sales model that they have chosen. They are the KMart of instruments. Doesn't mean that they are no good. It means that they get a lot of foot traffic. You purchase where you want. It's your guitar that you are buying. Just remember that the purhase is not the end of the game. You may need to have professional hel down the line as well, just like a car. Choose which store or internet site will give you what you need at purchase time and after.