The Prophet (peace be upon him) left Makkah by order of Allah to flee the persecution of Quraysh and thus to be free to practice Islam without fear.

Allah says in the Qur’an:

“And (remember, O Prophet,] how the disbelievers were scheming against you, in order to stop you [from preaching], or to murder you, or to drive you away: thus have they [always] schemed: but God brought their scheming to nothing – for God is above all the schemers.” (Al-Anfal 8:30)

“If you do not help the Messenger, then [know that God will do so -just as] God helped him at the time when the disbelievers drove him away, [and he was but] one of two: when these two were [hiding] in the cave, [and] the Messenger said to his companion, “Grieve not: verily, God is with us.” And thereupon God bestowed upon him from on high His (gift of] inner peace, and brought utterly low the cause of the disbelievers, whereas the cause of God remained supreme: for God is almighty, wise.” (At-Tawbah 9:40 )

Almighty Allah knows best.