Many clouds are flat on the bottom because as the air rises from the surface it cools, and at the saturation temperature it starts to condense, which is where the clouds start. Since the whole column is starting at the same conditions and going through the same process, it all condenses at the same height.
Clouds are formed when the temperature of the atmosphere reaches the condensation point (this is when it turns to water vapor). When this happens, the water vapor sticks to dust particles in the air and becomes visible. The temperature of the atmosphere usually changes(gets colder) as you go up, so only at a certain point can the water vapor droplets form. When you see the flat bottoms of clouds, you see where this point begins - this is the beginning of the proper temperature for water vapor to form.