Not all clouds do, by the way. But, clouds develop when rising air reaches its dew point and begins forming small droplets of moisture known as clouds. Therefore, since all, or most, clouds form at about the same altitude (depending on the dew point) they all tend to have the same baseline and appear flat. this is most noticeable with the boring
Stratus clouds. Any rising air tends to lift the body of the clouds unevenlingly producing the puffy tops
Here's some pictures of clouds with fluffy
bottoms
http://australiasevereweather.com/photography/ mammatus/mammatus_cloud0339.html .