Two big questions you've asked here, and I'll do my best to answer them as concisely as possible.

First, the Jacobite challenge was most definitely not only supported by Catholics. Roman Catholicism was closely associated with the Stuart dynasty, which reflected a deep lineage of familial confessional tradition and also represented a natural and tenured alternative to the terms of the Revolution settlement in 1688 as well as the ensuing constitutional establishment of Presbyterianism as the official state religion in Scotland. At the same time, anti-Catholic social and legal measures were enforced across Britain under the premise of tamping down 'popery' and what was considered by many to provide arbitrary power to a despotic lineage of kings. Jacobitism in Scotland was seen as a logical arm of Catholicism (and vice-versa) and a real threat to the faith-focused principles of Presbyterianism, and was at times cited as origo mali in Church of Scotland congregations and within public commentary.

Catholicism in England and Lowland Scotland during the early eighteenth century was primarily maintained by sparse, rural networks of landed gentry. In Scotland most of the Roman Catholic population came from the Highlands, but even there only a quarter of the clans held more than a divided adherence to that tradition by the start of the last rising. Webster's census in 1755 estimates around 19,000 Catholics in Scotland, and we can guess that around 4300-5300 Catholic Jacobite soldiers were raised in the 1745-6 rising. This represents only about 30% of a generous estimate of the Jacobite army at maximum strength and only 22-27% of the total Catholic population north of the border.

Jacobitism was also sustained by the Anglican Church in England and by non-juring Episcopalians in Scotland, the latter of who made up a distinct majority of Jacobite support by 1745. The north-eastern counties like Aberdeenshire, Banffshire, and Angus/Forfarshire, for instance, were traditional hotbeds of non-juring Episcopal Jacobite support and turned out easily more than half of all martial and civilian Jacobite engagement in the final years of its effective life. Episcopalianism was also a Protestant faith, but it shared a structure of power with Catholicism that gave unchecked control to centralized figures like bishops and, in the case of a Stuart restoration, the king himself. Non-jurors felt that the terms of the Revolution settlement were incompatible with their beliefs and, as intoned in their collective name, they refused to submit oaths of loyalty and abjuration to the Williamite and Hanoverian regimes. This naturally let many to consider Jacobitism as a desirable alternative to allow them to express their confessional freedoms, and concurrently attracted a great amount of animus from British government policies. Based upon prosecution results and reports of government reprisals after Culloden, rebel non-jurors were arguably treated worse than Catholics. All of this should make it abundantly clear that the civil war occasioned by the Jacobite challenge was definitively not one drawn down clean denominational lines.

Second, though the question of Jacobite motivation is a complex one that shifted significantly in its character through the course of its operational life, it is safe to say that the answer entirely depends upon who you are asking and about when and whom we are talking. I have written extensively about this topic here on Reddit and elsewhere through my body of work, so I would encourage you to take a deep dive as your time and interests allow. To sum it up in a concise answer, though, I can point to an excerpt from the link above:

"... independence-minded nationalist sentiment was a relatively small motivating factor in the bottom-up constituency of Jacobite supporters during the last rising. The Jacobite-Nationalist alignment has been subsequently force-fit due to the hot potato of the modern independence issue, and historical Jacobitism in the context of the eighteenth century has been distinctly misshapen by those in privileged positions who, in my opinion, should know better. This is certainly not a commentary on the viability of the nationalist agenda or the legitimacy of an independent modern Scotland...this vital issue should not be conflated with Jacobitism in a widespread historical tableau. They weren't and aren't the same things, however present a small degree of overlap."

An equally important question is what the elites, as well as the plebeians, were fighting for, up to and including the Stuarts themselves. Jeffrey Stephen has convincingly written about both James' and Charles' attraction to retaining regnal if not parliamentary union, despite what they repeatedly promised would-be supporters in their public declarations. That temptation was borne out by Charles' insistence on leaving a relatively secure Edinburgh and crossing the English border with London as the only permissible goal of his enterprise. This allows us to view the Jacobite challenge through a different lens – one that does not necessarily align the motives of the ideological visionaries with those of the popular citizens and country people who were targeted for support by Jacobite recruiters and then again targeted in reprisals by the British government.

Several suggestions for further reading follow:

• Jeffrey Stephen, ‘Scottish Nationalism and Stuart Unionism: The Edinburgh Council, 1745’, Journal of British Studies, 49:1 (2010), pp. 47–72.

• Alasdair Raffe, ‘Presbyterians and Episcopalians: The Formation of Confessional Cultures in Scotland, 1660-1715’, The English Historical Review, 125:514 (2010), pp. 570–598.

• Bruce Lenman, ‘The Scottish Episcopal Clergy and the Ideology of Jacobitism’ in Eveline Cruickshanks, ed., Ideology and Conspiracy: Aspects of Jacobitism, 1689-1759 (Edinburgh, 1982).

• Daniel Szechi, ‘Defending the True Faith: Kirk, State, and Catholic Missioners in Scotland, 1653-1755’ in Catholic Historical Review, 82:3 (July 1996), pp. 397-411.

• Thomas McInally, ‘Missionaries or Soldiers for the Jacobite Cause? The Conflict of Loyalties for Scottish Catholic Clergy’ in Allan Macinnes & Douglas Hamilton, eds., Jacobitism, Enlightenment and Empire, 1680-1820 (London, 2014), pp. 43-58.

• D. S. Layne, ‘Spines of the Thistle: The Popular Constituency of the Jacobite Rising in 1745-6’ (PhD thesis, University of St Andrews, 2016), pp. 58-62.

Hoping this has been of some help to you!

With best wishes,
Dr Darren S. Layne
Creator and Curator, The Jacobite Database of 1745