Question: "But thou, Bethlehem Ephratah, though thou be little among the thousands of Judah, yet out of thee shall he come forth unto me that is to be ruler in Israel; whose goings forth have been from of old, from everlasting." - Micah 5:2. The gospel of Matthew (2:5-6) claims that Jesus' birth in Bethlehem fulfils this prophecy. But this is unlikely for two reasons. "Bethlehem Ephratah" in Micah 5:2 refers not to a town, but to a clan: the clan of Bethlehem, who was the son of Caleb's second wife, Ephrathah (1 Chr.2:18, 2:50-52, 4:4). The prophecy (if that is what it is) does not refer to the Messiah, but rather to a military leader, as can be seen from verse 5:6. This leader is supposed to defeat the Assyrians, which, of course, Jesus never did. It should also be noted that Matthew altered the text of Micah 5:2 by saying: "And thou Bethlehem, in the land of Juda" rather than "Bethlehem Ephratah" as is said in Micah 5:2. He did this, intentionally no doubt, to make the verse appear to refer to the town of Bethlehem rather than the family clan.
Response: No, Micah was referring to the town of Bethlehem, in the southern part of Israel, which is also called Judah.
During Micah's time, there were two towns named Bethlehem. One was in Judah, the southern part of the land of Israel. The other was in the northern part of the land of Israel. The Bethlehem in Judah originally had been called Ephrathah. So, by using the phrase, "Bethlehem Ephrathah," he was making it clear that he was talking about the Bethlehem in Judah, rather than the one in the north.
There are several ancient Jewish writings that show that this verse was indeed considered a Messianic prophecy. Some of those writings are cited in our article at Bethlehem - Messiah's birthplace.
As for whether a skeptic believes that Micah was referring to the clan of Bethlehem rather than the town of Bethlehem in Judah, let me point out that in the book of Matthew, Jesus fulfills both requirements. He was born in Bethlehem in Judah, and as a descendant of King David, he was also a descendant of the clan of Bethlehem.
As for skeptic claim that the person described in Micah 5 was supposed to be a military leader who defeats the Assyrians, there are several problems with the wording of that claim. But let me point out that the book of Matthew, which is the book in question here, makes it clear that Jesus will return to complete his mission.
Whenever there is disagreement over the interpretation of Bible verse, skeptics like to assume that the believers have "twisted" their interpretation of it. It would be smarter and wiser for people to question both the believer and the skeptic. Otherwise, you're just blindly putting your faith in the skeptics.
More information about Micah 5:2 can be found here:
Bible prophecy: The Messiah would be born in Bethlehem
A detailed look at Micah 5:1-2 and some objections that skeptics have