Why do cookies go flat in baking?

Answer 1

that way the cookies can get softer Cookie dough contains a lot of grease (lard, vegetable shortening, butter) and they melt and flow as they bake. At the point where the gluten and starches cook, the sugar carmelizes and the moisture is driven off they stop spreading.

Answer 2

According to Alton Brown of Food Network's GOOD EATS -- it is the sugar content that determines whether a cookie is chewy or crispy. White sugar leads to crispier cookies and brown sugar to chewier. So, to some extend, more brown sugar in the recipe can also make the cookie spread more (flatten out). That is why the Toll House recipe calls for equal amounts of the two sugars.
Also, the leavening -- baking soda and/or baking powder help a cookie rise. Old baking powder may not work as well as fresh, especially if it has acquired any dampness (i.e. does it clump together in the can, or even need to be scraped out?). Baking powder reacts with liquids to create bubbles in the batter and help it rise.
Last, the type of shortening you use in the cookie will affect how it spreads. A shortening like Crisco will spread far less than butter will.
When it comes to Chocolate Chip Cookies, it is the one recipe I follow as closely as I can -- I tend to be a little loose with measurements except for chocolate chip cookies that "need" (well, in my mind) to be a certain way when they come out of the oven -- the right height and spread, crispiness/chewiness ratio, etc. -- come only from following the recipe on the bag. Never found any other chocolate chip cookie recipe that works for me.