There are loads of sites and Books by Muslims that states that Muhammad was persecuted by the Meccans for preaching Islam, and this led Prophet to leave Mecca and Move to Yathrib (Medina). This gives Muslims a chance to create a myth; that Prophet fought his fight in self-defense. However the Historye of Muhammad, written by Muslims themselves is a stark denial to this fact. If at all, Muhammad was persecuted, we need to know the reason as to why he was persecuted. The reason for his persecution is important to be able to pass any judgment on him. Today we see all Governments of different countries persecute Terrorist Organizations and Drug Dealers, but those Governments are not to be blamed for persecuting or prosecuting these Organisation. In the same way, we need to see why Muhammad and other Muslims were persecuted, if really he was?
The very first thing I notice in Islamic history is that Quraysh was very Tolerant. As one of the Muslim biographer says, “Abu Talib made no objection to Islam of his two sons ]a’far and ‘Ali, but for himself he said he was not prepared to forsake the religion of his forefathers; ‘Abbas was evasive and Hamzah uncomprehending, though both assured him of their unfailing affection for him personally.” 
This shows the head of Quraysh was a tolerant man, he had no objection when his two sons embraced Islam.
When Muhammad started mocking and insulting the religion of Quraysh, Quraysh went to Abu Talib, and requested him to ask Muhammad to stop insulting them. Quraysh said, “0 Abu Talib, thine is a high and honourable position amongst us, and we have asked thee to hold in check thy brother’s son, but thou hast not done so. By God, we will not suffer our fathers to be insulted, our ways scoffed at, and our gods reviled.” 
The above quote however does not prove that Muhammad was persecuted, Muhammad used to insult and abuse gods and the religions of the Qurayshies. Quraysh begged Abu Talib to stop his Nephew . Another source says, “ the Quraysh went to Abu Talib, a highly respected elder who was the Prophet’s uncle and tribal protector, and demanded that he put an end to Muhammad’s behavior, whom they accused of cursing their gods, denouncing their forefathers and insulting their religion. “ 
Quraysh had a reason to be negative toward Muhammad. The Prophet cursed their gods, denounced their forefathers, and insulted their religions. But they did not fight directly; rather they requested Abu Talib to stop Muhammad. But Abu Talib failed to stop Muhammad. Even so, this did not make Quraysh attack Muhammad. They still waited and hoped for peace. Quraysh, sent another person, Utbah to offer Muhammad anything he wanted so that he can leave them in peace.
Utbah went to the Prophet and said, “Son of my brother,thou art as thou knowest a noble of the tribe and thy lineage assureth thee of a place of honor. And now thou hast brought to thy people a matter of grave concern, whereby thou hast rifted their community, declared their way of life to be foolish, spoken shamefully of their gods and their religion, and called their forefathers infidels. So hear what I propose, and see if any of it be acceptable to thee. If it be wealth thou seekest, we will put together a fortune for thee from our various properties that thou mayst be the richest man amongst us. If it be honour thou seekest, we will make thee our overlord and take no decision without thy consent; and if thou wouldst have kingship, we will make thee our king; and if thyself thou canst not rid thee of this sprite that appeareth unto thee, we will find thee a physician and spend our wealth until thy cure be complete.” Before Utbah went to prophet, read what made Utbah go to Muhammad. In a meeting with other Chiefs of Quraysh, Utbah said, “‘Utbah ibn Rabi’ah. “Why should I not go to Muhammad,” he said, “and make certain offers to him, some of which he might accept? And what he accepteth, that will we give him, on condition that he leave us in peace.” 
We can see what was the grave concern with the Prophet’s tribe. Muhammad broke the peace of his Tribe, and he was also a big danger for the basic livelihood of his tribe, which was through pilgrimage to the Kaaba. On one occasion Quraysh decided that outside the town all the roads by which Mecca was approached ( by Pilgrims) must be manned, and that visitors must be warned in advance to be on their guard against Muhammad. This was done because Quraysh had a high reputation of hospitality, not only as regards food and drink but also because they made every man feel welcomed, both him and his gods. But this year there was the threat that pilgrims will hear their gods insulted by Muhammad and his followers, and they would be urged to forsake the religion of their forefathers and to adopt a new religion which appeared to have numerous disadvantages. 
Prophet even failed to prove his religion, which is evident from Many Meccans verse while at the same time he abused their religions, forefather and gods. Then Quraysh wrote a decree institutinging a boycott of the Hashim and al-Muttalib sub-clans: marriage, and all forms of buying and selling, between the rest of Quraysh and the two sub-clans was completely suspended, such that not even basic provisions could be secured. 
This boycott continued for three years. During this period Muhammad earned few followers in Medina, who used to visit Muhammad during each Pilgrimage season. Finally, all his followers met with the Prophet in secrecy at ‘Aqaba, in nearby Mina under cover of night, to make the following pledge: (1) Not to associate any partners with the one true God, Allah; (2) To obey the Prophet in all righteous matters; (3) To refrain from stealing; (4) And adultery; (5)And infanticide; (6)And slander. In the following year a larger delegation (over seventy, including two women) again met with him during the pilgrimage season and invited him to migrate to Medina. On that night they proclaimed the second pledge of ‘Aqaba, with a new added clause (7) To protect the Messenger in the same manner as they would protect their own women and children. After this Muslims started Migrating to Medina. 
I don’t find any persecution from Quraysh, and he was only boycotted, but for a reason. Now, Gandhi asked Indians to Boycott the British when they ruled India. This does not make Gandhi a cruel man and in the wrong. By the same token, Quraysh boycotted Muhammad since he was a threat to their peace, abused and insulted their forefathers and religions, without proving his own religion to be correct. He also was a threat to their livelihood, which they earned from servicing Pilgrims. This Muslims claim of persecution in Mecca is no more than a mirage.
 Muhammad- His life based on earliest source, by Martin Lings. Pg no- 50
 Historical development of the Qur’an, by Cannon Sell, Pg no-5
 The History of Qur’anic Text, By Muhammad Mustafa Al- A’zami, Pg no- 28
 Muhammad- His life based on earliest source, by Martin Lings. Pg no- 60-61
 Ibid, Pg no- 53
 The History of Qur’anic Text, By Muhammad Mustafa Al- A’zami, Pg no- 29
 Ibn Hisham, Sira, vol. 1-2, p. 433 to 442