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.
On the lighter side, one could say that "Venus" is much easier to pronounce and read than "Aphrodite". On the serious side, the name differences are a result of the Greco-Roman transition as the Romans slowly exerted their own cultural influences, with a blending of some of the Greek culture. Mythology becomes a dynamic puzzle remembering the name changes! It's also interesting to note the artistic interpretations of Aphrodite and Venus presented through the sculptures, and paintings of each during its time: depictions from Hellenistic Greece , Classical Greece, Greco-Roman, and Roman cultures. The Venus of Milos in question was based on an interpretation of the earlier Greek statue of Aphrodite de Milos from the 4th century b.c. Milos is the Greek word for "apple". In the mythology of Aphrodite, the apple is an important symbol. The Venus de Milo statue when it was discovered in 1820, created a spark in the culture of Paris at the time. The history reflects that the Turkish government's sale of the statue to France, as a gift to Louis inspired tall tales and whispers of conspiracies. I do hope that this response inspires you to have fun learning more about this statue!