While still a young man, Jonathan Swift desired to become a part of the Church of England. At the age of 27, he took his orders and became an Anglican priest. The Earl of Nottingham took a dislike to Jonathan, for whatever reason, and blocked his appointment to bishop.
Being of Irish descent, Swift also devoted his time to the society and politics found in Dublin. He was outspoken about England’s treatment of the Irish, and opposed the War of the Spanish Succession (1700 - 1715). The Duke of Marlborough, however, was a primary influence on England’s participation in that war. The two men found themselves to be fervent political opponents.
Since it is considered that many of Swift’s characters had their foundation in people from his own life, it can be conjectured that the character of Skyresh Bolgolam was based on either the Earl or the Duke. Neither of the two had any particular fondness for Swift, nor did they have reason to dislike him. He was merely an unfortunate being over whom they could exercise their need to be disagreeable.
So, one may conclude, that there was no valid reason for Bolgolam to dislike Gulliver. It appeared to be a matter of personal enmity.