The terms Jacobite and Whig come up often in Kidnapped, but to the modern reader, these words have lost most, if not all of their meaning. Since Kidnapped focuses on a historical event, the murder of Colin Campbell of Glenure, it makes sense that it contains much historical and political information.
The people known as "Whigs" were those who were loyal to the current English government, particularly its king. Whigs were Protestants, as all English subjects were supposed to be. Almost all of England, and most of Lowland Scotland, were Whigs at the time that the novel takes place (1751).
The Jacobites were a party formed after the Glorious Revolution of the late 1680s. When William and Mary retook the throne from James II, the Scottish king of the Stuart line, the supporters of James—mostly Scots—became known as Jacobites. For nearly a century after the Glorious Revolution, the Jacobites attempted to put James and his heirs back on the English throne, primarily through a series of rebellions and battles. James had tried to restore Catholicism to England, but the Glorious Revolution had soused his intentions. The Jacobites, however, remained primarily Catholic, which put them out of favor with most in the English government.
By 1750, the Jacobites had lost a number of important battles, and would never really be a threat to the English government again. Most of the Jacobites were now lived in the Highlands of Scotland, while the Lowlanders were assimilated into the Whig party by their closer proximity and greater trade with England. In order to quell the rebellious Jacobites, the English government began to try and break up the clans that were to be found all over the Highlands. The Campbell clan, which was loyal to the Whigs, became instrumental in this task, and many other clans, such as the Stewarts, Alan's clan, saw the Campbells as having betrayed them. The Campbells soon controlled all the courts and other offices in the Highlands, and Colin Campbell was particularly ruthless in his behavior toward the other clans. This led to his murder, the central event in Kidnapped.
Stevenson, who has an affinity for the Highlands, may have written Kidnapped with the intention of helping repair the negative image that the English had created of the Highlanders, and give them their due respect. This can be seen in the oddly noble manners of Alan and James of the Glens, both of whom David comes to respect.
The idea of inheritance, and particularly, primogeniture, the idea that the eldest son always inherits an estate, plays a significant role in Kidnapped. The most basic plot of the novel involves David returning to the House of Shaws to claim his inheritance after his uncle tries to scheme him out of it.