There are four separate reasons, I think. Disclaimer: I know less about Scotland than I do about England, but this is in my time period range and interconnects with England, so I'm giving it a go.

Those reasons are the relative lack of violent imposition, the identification of Catholicism with foreigners- specifically the French, the support of local lords, and better English intervention measures.

Firstly, in Margo Todd's "The Culture of Protestantism in Early Modern Scotland" (2002) she notes that the work of Gordon Donaldson in "A Backward Nation?" (Scotland's History: Approaches and Reflections, 1995) shows the difference in executions for being Catholic or Protestant between England and Scotland in the transition period; hundreds compared to less than fifty. This element was helped by the strength of the other factors which reduced the point of violence, but it is nonetheless notable and likely relevant that there was less top-down violence to impose changes. Ireland suffered substantially from English attempts to impose Protestantism. While the English had traditionally ruled very laxly in Ireland, barely controlling it, when Henry VIII decided to increase his control, religious violence over the introduction of Protestantism became a feature that would haunt Irish history for the next four hundred years. That violence did not work as efficiently as the Scottish reformation. Margo Todd argues for the significance of Scottish Kirk's emphasis on educated clergy and informed laity, which was note unique among Protestants but the Scottish quickly became quite organised and effective at religious campaigning.

Secondly, it's significant that France, which had a close relationship with the Scottish monarchy, became one of the primary forces trying to keep Catholicism in Scotland. This is most significant during the regency of Mary, Queen of Scots' mother, Mary of Guise, a very visibly French Catholic who suffered the final loss against the Lords of the Congregation. A foreign woman and her absent daughter, married to the French heir, was not an inspiring image of Scottish leadership; which involved controlling feuding male warrior lords. Jenny Wormald in "James VI and I: Two Kings or One?" (1983) says that 16th century Scottish kingship depended on social contact, even more so than other Early Modern governments; which in places like England and France were more complex and controlling. She highlights that while Henry VIII's use of parliament in the English Reformation set a precedent that would lead to tension, the Scottish parliament went one step further and passed it's reformation in 1560 in direct defiance of the Crown. So, a foreign woman was at a disadvantage in a system that relied heavily on keeping the support of the lords. Mary's use of French troops and French advisors was understandable but backfired in the long-run (Andrew Lang, "John Knox and the Reformation", Ebook edition 2012). In contrast, the Irish experience of Catholicism was that of their native religion that was being threatened by foreign forces who wished to control them. Henry VIII briefly established the idea of the Church of Ireland in his reformed styles, but for the most part the Anglican Church in Ireland was just the Anglican Church. The leftover elements of leniency in the English not trying that hard to convert the whole population meant what attempts they made were doomed.

The support of local lords is key here, as you can see. They not only contributed to the military outcome, they were also involved in the propaganda. If more of the Scottish lords had decided to support Catholicism, they could have helped encourage their tenants to hold to it instead of the reverse. And they certainly would not have voted to overturn if they have been on side. In contrast, the Irish lords actively led rebellions against Protestantism, and quite few of the Irish lords ever converted to Protestantism in the 16th century. The largest population of Protestants that developed in Ireland was in the north and a good portion of that was from Scottish and English planters (settlers). As noted before, there were elements of both historical concession and the rise in sudden oppressive violence, which Joseph Ruance in "Majority–Minority Conflicts and their Resolution: Protestant Minorities in France and in Ireland" (2006) notes became two strategies. The second, violent one grew over time in response to resistance, while at the same time it is worth noting than the more loyalist Anglo-Irish lords had almost as much autonomy as the notoriously rebellious Gaelic ones. In 1640 the fear that the new parliament session would have the aggressively Protestant Commons encourage the King to bring a new clamp-down caused the Anglo-Irish to side with the Gaels in a new rebellion; which led to Oliver Cromwell's infamous Irish campaign to suppress them.

Finally, it's also significant than Elizabeth I's hesitance to support a rebellion against a divine-right monarchy, and especially her hesitance to be seen doing so, led her to use covert measures. The minimal and secretive English support worked well for the Lords of the Congregation's justification that Catholicism was being imposed by France because it prevented any arguments that England was doing the same. In contrast, the English religious and military campaigns in Ireland were very open and the legal changes openly imposed by the English crown. This meant the anti-colonial narrative was easy.

So, in conclusion the Scottish Reformation worked well for reasons that relate to each other. They were less violent, primarily local and independent, they controlled the crucial local power bases, and the English support was wisely subtle. The Irish situation however, was marred by the idea that never quite died among the English that the 'barbarous" Irish should be easy to control, no matter how much they caused trouble. As a result, although subtler and more lenient measures were used, the scale of the violence was too much to allow them to work and be focused upon. A lack of patience was the ultimate doom of Irish conversion attempts.