This is a great question. Let me start off with some background information and give you two reasons why the Roman name is more popular.
The statue was created sometime in the early 100s B.C. The sculpture is 6 feet 8 inches high and the arms has been lost. It is thought to be the work of Alexandros of Antioch, but we cannot be absolutely sure with anything that old. It is now on display at the Louvre in Paris.
Now as for why it is better known as Venus instead of Aphrodite. There are two reasons for this. First, as you know Milos is a Greek city, but after the Roman conquests of the Greek East, these cities became more and more Romanized. Moreover, when the gods of Greece and Rome came together, often the Greek counterparts took on Roman names. Hence, Aphrodite became Venus. This was fairly common.
Second, from a historical perspective, when ancient discoveries are mediated through the the West, the names that are used are Romanized. Hence, it makes sense that the sculpture is now known as Venus instead of Aphrodite.