Same reason I never understood the "Gold Pressed Latinum" nonsense. Even if you couldn't replicate it, what would you buy with it? Everything is free.
Because not every culture used replicators to the same extent as Federation cultures did. Remember who were the biggest proponents of latinum-based economics? The Ferengi, who were all about gaining wealth by pretty much any means; their entire culture is built around gaining material wealth. A replicator needs feedstock in addition to energy, and those don't necessarily HAVE to be free.
Voila, there's your money-based economy in the face of replicator technology.