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Early Christians were ruthlessly persecuted by the Roman Empire who believed that their religion was subversive. For example, in Rome (among other places), which was the capital of the empire, they were often used as fodder in the "games" at the Coliseum to feed the lions.
Saint Peter, one of the original apostles of Christ and regarded as the first "pope" who established churches on his journeys, is traditionally held as one of Rome's victims under the Emperor Nero who crucified him. When he said that he did not deserve to die as Christ did, he was crucified upside down. His remains were then buried in Rome.
Centuries later when Emperor Constantine took control of the Western Roman Empire, he ended the persecution of the Christians via the Edict of Milan in 313 AD.
The bishops of Rome were also seen as successors to the papacy which traces its lineage to Saint Peter. With their freedom under Constantine, and following Saint Peter's work in the heart of the empire that had once persecuted them, Rome became an important part and eventually the mecca of the Roman Catholic Church.