I am not an atheist but I have looked in ancient history and philosophy and the development of religion and my research has led to be question whether Jesus as presented in the New Testament was a real, historical person. Christianity may have begun with a mystical Jewish sect called the Essenes in the 1st to 3rd century BCE. The Babylonian Talmud speaks scathingly of a person named Yeshua (Jesus) who in some ways resembled the Biblical Jesus and was said to be an apostate to the Jewish faith, a miracle worker (a mage or sorcerer, that is), and the illegitimate son of a Roman soldier. But whether this information is legendary (a rant against Jews who were following a proto-Christian ideal) or a "real" story about a "real" person is controversial. Someone resembling Jesus (named Jesus or some derivation of the name) was said to be or documented as being stoned to death and hung on a tree in the 1st century BCE for being a miracle worker and a political provocoteur.
The earliest form of Christianity, arising from Essene Judaism, was Gnostic. It did not necessarily think of Christ as an historical person but as an ideal. This form of Christianity was later (300 CE or so) rejected by politicians who decided to adopt and standardized Christianity and force it on everyone else (leading to the Dark Ages, the Crusades, and the Inquistion, etc.)
But back to the pagan, pre-Christian Roman govt.: The Roman government was very particular about religious and spiritual observances because cosmic order was believed to be kept by appropriate ritual interaction between the gods and people. If something went out of whack, it meant the end of civilization as far as the Romans were concerned. Roman officials not only cracked down on Christians but on other cults (like the cult of Dionysius, which ended when the Roman govt. slaughtered most of its adherents in a massacre.) The Romans supposedly viewed Christ as a magician/sorcerer and Christianity as a form of black magic. As far as the Roman officians were concerned, Christians worshipped a sorcerer and they took the symbol of a form of torture and death--the crucifix--as their holy symbol. (To put this into perspective, think of how Christians view pagans who wear pentacles or worship horned gods. --With fear, revulsion, and threat even if it is unfounded. The Romans thought of Christians in the same way, and thought they were threats to society. )That is why the Romans persecuted Christians and others.