Simply put, the fact that among the believing community only Paul had to flee from Jerusalem goes on to emphasize that he was, indeed, preaching something different from what the Apostles preached in Jesus’ name. But why did he have to flee to Caesarea and then to Tarsus (Acts 9:30)? Why couldn’t he simply flee to Galilee or Perea, just as Jesus did when he got into trouble with the Jerusalem authorities? If he did so, he may have been able to stay more in touch with the Apostles and eventually return to Jerusalem when the climate was more accommodating.
The answer to this question seems to me to be twofold. First of all, Jesus had not only commissioned Saul/Paul to preach to the Jews but also to the gentiles. While he could preach to the Jewish community throughout much of the Roman Empire, he could not very well reach many gentiles while staying in Jerusalem or even in Galilee for that matter. No, Paul was destined to travel away from Judea and the Lord worked out Paul’s activities in Jerusalem to fulfill his plan for Paul and the emerging Church (or Body of Christ—which included both Jew and gentile alike).
Secondly, we need to understand that the Jerusalem authorities were composed of Sadducees, a powerful Jewish wealthy class, and Pharisees, a zealous and religious group who had risen from the Jewish middle and, perhaps, even from the lower classes. The Sadducees’ power was founded upon their wealth and the political support they received from the Roman authorities; but the Pharisees arose out of the masses and derived their authority from the support of the Jewish people, so this second group was very sensitive to public opinion. If divided, the ruling authorities in Jerusalem could do nothing (cp. Acts 23:6-10 and Acts 5:30-40). Normally, the people supported the Apostles, perhaps due to the fact that so many miracles were done on behalf of the poor and needy (cp. Acts 5:12-18 and Acts 5:25-26). However, the people’s loyalty could be turned, if the Sadducees and Pharisees had a common enemy and if somehow grievous charges contrary to the Jewish faith could be made publically against the believer—whether true or not. Men conspired to lie to the people against Stephen (Acts 6:11-12), and through a misunderstanding years later, Paul was accused of blasphemy, and the multitude (the Jewish people) tried to kill him (Acts 21:27-31), even though he had recently brought a large offering to Jerusalem for the poor (Acts 24:17).
What seems to have occurred in Jerusalem, during his first visit there following his conversion, is that Paul had stirred up official opinion against himself. It may have taken a few days, perhaps a little longer, to stir up the people, but a conspiracy against Paul’s life was in the making (Acts 9:29; cp. Acts 6:10-12). Paul was warned in a vision that he had to flee (Acts 22:17-21), but where would he be safe?
The influence of the high priest and the Jerusalem authorities could be made to press against any man hiding out anyplace where the power of the Jewish high priest was respected and obeyed. Nevertheless, Caesarea was not a Jewish city. It was composed largely of gentiles, and it was the seat of Roman authority for Judea. Although the high priest’s authority was supported by Roman officials in the eastern Empire, this support did not extend to extradition of its citizens from places it governed like the city of Caesarea. Believers were relatively safe there, and this is probably why Philip, one of the original seven (cp. Acts 6:5 and Acts 8:40 with Acts 21:8), had settled there, escaping the persecution following Stephen’s death. The believing community took Paul there where he would be safe and able to freely obtain passage to his hometown of Tarsus (Acts 9:30).