The simple answer is for the same reasons that all Protestants broke from the Church, only at a different pace, in a different manner, and with different leaders than the rest of the Protestant world. The Church had become corrupt and looked out for it's own financial and political interests, at the expense of everyone else.

The Church first came to Scotland when the Irish missionary St. Columba founded a monastery on the island of Iona off the west coast of Scotland to convert the Picts and Scots. Monks from the island worked to convert the people of Scotland for decades culminating in St. Cuthbert in the mid 7th century.

The Church languished in Scotland for the next several centuries after Cuthbert for a number of reasons. Viking raids, wars between the Scots, Normans, Britons and Angles all distracted the people, and there were no strong advocates of the church in Scotland during this time. It wasn't until David I (1124-53) that the Church took a strong hold.

Much of Scotland was thinly populated and it's villages distant from each other, which made the establishment of strong parishes difficult. Scotland was a long way from Rome, which allowed the local Church to become lax. And the Church in Scotland fell down the same path of avarice, venality and luxuriousness seen on the Continent, collecting money, lands and influence. Scotland was also far enough away to not feel the effects of the Reformation, although a few Lollards or followers of John Hus were executed.

By the mid-16th century, Scotland had been allied with Catholic France for nearly two centuries. However much of the nobility began to advocate an alliance with Protestant England. As distasteful as this must have been to many, the French had too often used Scotland to advance French interests. England had become a very populous country, and an English alliance could mean peace and prosperity vs. continual defeat and conquest. At the time the kingdom was held under Regency for the young Mary Queen of Scots after the death of James V. The Nobles also saw it as an opportunity to gain enormous wealth by seizing Church property much as Henry VIII had done in England. That opportunity alone turned many nobles instantly into Protestants. Protestantism also meant that they would be out from under the thumb of Consistorial courts and appeals to Rome which tried their patience and their purses.

The Reformation truly began in Scotland on New Years Day in 1559 when a copy of the Beggars' Summons was posted on the gate of every Church in Scotland.

The blind, crooked, lame, widows, orphans, and all other poor visited by the hand of God as may not work, to the flocks of all friars within this realm, we wish restitution of wrongs past and reformation in times coming.

Concluding as follows:

Wherefore, seeing our number is so great, so indigent, and heavily oppressed by your false means that none taketh care of our misery and that it is better to provide for these our impotent members which God hath given us, to oppose to you in plain controversy than to see you hereafter, as you have done before, steal from us our lodging and ourselves in the mean time to perish, and die for want of the same; we have thought good, therefore, ere we enter into conflict with you to warn you in the name of the great God by this public writing affixed on your gates where ye now dwell that ye remove forth of our said hospitals, betwixt this and the feast of Whitsunday next, so that we the lawful proprietors thereof may enter thereto and afterward enjoy the commodities of the Church which ye have heretofore wrongfully holden from us: certifying you if ye fail, we will at the said term, in whole number and with the help of God and assistance of his saints on earth, of whose ready support we doubt not, enter and take possession of our said patrimony, and eject you utterly forth of the same. Let him, therefore, that before hath stolen, steal no more, but rather let him work with his hands that he may be helpful to the poor.

The English Protestant reformer John Knox arrived in Scotland from exile and imprisonment at this moment. His passionate preaching ignited the fervor of commoner and noble alike. One passionate sermon led to a riot at the Church in Perth. This led to the Queen regent requesting a French army to punish Perth. But a Protestant army was raised and with the help of Queen Elizabeth I of England defeated the French leading to the Treaty of Edinburgh.

Scottish Parliament made it official that the Church of Rome was no longer the official Church of Scotland on July 10, 1560. Mary ascended to the throne in 1561 and as a fervent Catholic initiated a battle between Kirk and Crown, which was basically a fight between herself and John Knox. Mary was not up to the task and was imprisoned when she fled to London in 1567 to seek the support of her cousin Elizabeth.

This allowed the Kirk to firmly establish Protestantism and the Presbyterianism in Scotland in one of the quickest, least violent transformations in the Reformation.

The Anglican Settlement and the Scottish Reformation - F. W. Maitland

A Source Book of Scottish History - W. Croft Dickinson, Gordon Donaldson, and Isabel A. Milne