First, Bethlehem was most likely no bigger than Nazareth, so how many babies of that age would there be in a village of five hundred or six hundred people? Not thousands, not hundreds, although certainly few. Second, Herod the Great was a bloodthirsty king: He killed members of his own family; he executed lots of people who he thought might challenge him. So the fact that he killed some babies in Bethlehem is not going to captivate the attention of people in the Roman world.
And third, there was no television, no radio, no newspaper. It would have taken a long time for word of this to spread, especially from such a minor village way in the back hills of nowhere, and historians had much bigger stories to write about. I don't think it was much of a story, at least not in those days. A madman killing everybody who seems to be potential threat to him; that was business as usual for Herod. Of course, later as Christianity developed, this incident became more important, but I would have been surprised if this had made a big splash back then. You have to acknowledge the bloody landscape of the ancient Palestine.
Jesus' crucifixion is factual. Even an extremely liberal like Crossan says: "That he was crucified is as sure as anything historical ever can be." Skeptic James Tabor says, "I think we need have no doubt that given Jesus' execution by Roman crucifixion he was truly dead." Both Gerd Ludemann, who's an atheistic New Testament critic, and Bart Ehrman, who's an agnostic, calls the crucifixion an indisputable fact. Why? First of all, because all four Gospels report it. Let me clarify something: For the purposes of examining the evidence, I'm not considering the Bible to be inerrant, inspired, or scripture of any kind. I'm simply accepting it for what it unquestionably is, a set of ancient documents that can be subjected to historical scrutiny like any other accounts from antiquity. In other words, regardless of my personal beliefs, I'm applying the same historical standards to it that I would apply to Thucydides or Suetonius.
Now, beyond the four Gospels, we also have a number of non-Christian sources that corroborate the crucifixion. For instance, the historian Tacitus said Jesus "suffered the extreme penalty during the reign of Tiberius." The Jewish historian Josephus reports Pilate "condemned him to be crucified." Lucian of Samosata, who was a Greek satirist, mentions the crucifixion, and Mara Bar-Serapion, who was a pagan, confirms Jesus was executed. Even the Jewish Talmud reports that "Yeshu was hanged." Yes, Yeshu is Joshua in Hebrew; the Greek equivalent is translated as Jesus. And in the ancient world to be hung on a tree many times referred to a crucifixion with the Pentateuch, which says that "anyone who is hung on a tree is under God's curse."
This fact is as solid as anything in ancient history: Jesus was crucified and died as a result. The scholarly consensus, again, even among those who are skeptical toward the resurrection, is absolutely overwhelming. To deny it would be to take a marginal position that would get you laughed out of the academic world.
Edit: I appreciate your response and thank you for taking this seriously, but for the sake of the argument let’s suppose that the story about Herod ordering the extinction of all the young ones in Bethlehem was a later, legendary addition to the Gospel, despite the fact that it has been shown that a story must be passed around orally for about two centuries in order for legendary material to creep in during the ancient Palestine, what would that mean for the truth of Christianity? I don’t know about you, but to me it would mean nothing, since the Gospel message is centered on the testimony of Jesus’ resurrection and not the testimony of Herod's order. That’s why Paul, who started out as an enemy of the early Christ-movement and underwent an inexplicable conversion to that very movement, said, “And if Christ has not been raised, your faith is worthless; you are still under condemnation for your sins. In that case, all who have died believing in Christ have perished!"
When historians determine whether a historical event happened or not with only one source available they usually give the benefit of the doubt to the writer of that source, unless further evidence proves otherwise. When it comes to the New Testament documents, however, many people use a whole different set of criteria than they would use on secular documents. Considering that Herod’s ordering the extermination of the young ones in Bethlehem is not a supernatural event and is in line with his evil nature known from other sources, I think historians would give the benefit of the doubt to the writer of that Gospel. But, again, even if this event is nothing more than a later fabrication, it has hardly any bearing on the reports of the resurrection of Christ, which is the foundation of my faith.