Because Ireland was effectively ruled as a colony, politically separate from England but completely subordinate to it. The native Irish were treated pretty horrifically - in fact, Theodore Allen in his book The Invention of the White Race makes a strong analogy between English racism towards the native Irish and the attitude of white colonists to Native Americans and African slaves in North America. The religious dimension added by the Reformation only made that worse and transformed it into a Protestant-Catholic conflict.

Scotland was never remotely on the same level. Unlike Ireland or Wales (and some would add Cornwall, and even Northern England), it was clearly a partner within Britain, rather than a part subjugated and forcibly controlled by England, like the others. Scotland might clearly have been the lesser partner, but it was a partner nonetheless. While after the Jacobite Rebellions, there was a pretty significant suppression of Scottish Gaelic identity to bring it more into line with England, it was never on the same level as Ireland.

And of course, there was no Great Scottish Potato Famine.

Scotland's relationship with England was very different from Ireland's relationship with England and later the United Kingdom.

The first thing that it is worth noting is the difference between "English" and "British." Scotland is a part of the island of Great Britain, just as England is. So to a certain extent, Scotland throwing off "British reign" wouldn't make much sense.

The origins of the political entity that is the United Kingdom provide evidence as to why Scotland and Ireland's history are so different. The "United" part of "the United Kingdom" refers to the union between the Kingdoms of England and Scotland that took place in 1707 with the signing of the Acts of Union. Rather than England conquering Scotland, the two countries voluntarily signed a treaty that made them into a single kingdom.

The reason why the Acts of Union was possible is that the Kingdoms of England and Scotland had already been ruled by the same dynasty - the Stuarts - since 1603 (with an interruption, of course). The Stuarts were a Scottish dynasty, with King James VI of Scotland being selected to become King James I of England following the death of Queen Elizabeth I. In practice, the Stuarts ruled out of England, which, with its vastly greater population, would be de facto the more important of the two countries, but this was clearly not the case of England subjugating the Scottish.

The Irish (and the Welsh), on the other hand, were subjugated through continuous warfare (as well as a hefty amount of politics). Cromwell's conquest of Ireland (Ireland had been effectively brought under English control by the Tudors, but they rebelled in 1641) was notoriously brutal.

This is not to say that the English never tried to suppress Scottish identity (even by force), but the difference in scale between what the Scottish and Irish experienced is significant.

Both of the answers on this thread have missed out the crucial part played by religion in the relationship between England, Scotland and Ireland. The ill treatment of the native Irish by the English (and indeed the Scottish - but more on that later) was down to the fact - not that they were Irish - but that they were Irish Catholics. By the end of the 16th century Scotland had embraced Presbytarianism and England had stumbled, almost accidentally, into Anglicanism. These two streams of protestantism were a far cry from one another ideologically, but shared in common a deep distrust of the Church of Rome. In some ways Catholicism was the red scare of its time. The two major European powers at the time, France and Spain, were Catholic, and so the religious struggle against Catholicism was also seen by British Protestants in terms of a national struggle against foreign influence and domination.

Obviously this didn't leave Ireland, with it's mainly Catholic population, in a good place. English settlement of Ireland was mainly a concerted and ill-fated effort to supplant the native Catholic population with Protestants. Religious fear and paranoia drove the conflict between the groups to extremes of brutality. The Scots played their part too. Most of the Protestant settlers who came to Ulster in the 17th century were Presbytarian Scots, and that particular effort was conducted by James I of England, who was also of course James VI of Scotland.

I'm late to this thread (curse time zones!) but I'll try to add a bit from an early modernist's perspective to support and supplement the answers already given by /u/JFVarlet, /u/lngwstksgk, /u/anotherMrLizard, /u/Second_Mate, and /u/eighthgear.

There has already been plenty of mention made of the Union of the Crowns (1603) and of the political Act of Union (1707) to describe a sense of relative equality between Scotland and England that didn't exist between Scotland, England, and Ireland so I won't go into that here, rather, I'm going to discuss cultural factors in play as well some political issues that have yet to be mentioned.

Before James VI/I inherited the throne of England, Scotland was an autonomous nation with an established and widely-acknowledged monarchy, and Scotland as a nation had managed to withstand previous English attempts at conquest and forceful union. The Scottish Wars of Independence (1296-1328 and 1332-1357) are well known thanks to the wildly inaccurate film, Braveheart but what is not as well known is Henry VIII's campaigns against Scotland in his attempt to forcefully wed Mary, Queen of Scots to his son, the future Edward VI. It was because of this Tudor policy that Mary was sent to France to be married to the French dauphin instead...because Scotland refused to be cowed into a forced union with England. Union was inevitable, however, dynastically speaking, due to the failure of the senior Tudor line. When Elizabeth I refused to marry and bear children, this left James VI/I her closest living relative from the direct Tudor line. James was the great-grandson twice over of Margaret Tudor, Henry VIII's sister. Margaret had married, first, James IV of Scotland and with him had borne James V of Scotland who was the father of Mary, Queen of Scots. But, Margaret remarried after Flodden and with her second husband, Archibald Douglas, earl of Douglas, she had a daughter, Margaret. Margaret married Matthew Stewart and together, they were the parents of Henry, Lord Darnley who became Mary, Queen of Scots' second husband and was the father of James VI/I.

Thus, genealogy lesson aside, when James VI/I united Scotland and England under the mantle of his personal rule, the union was effected not by conquest but by inheritance which is a significant fact to keep in mind. Ireland, by contrast, was never even viewed as a potential equal. It was conquered, first, by the Normans in the thirteenth century, and again by the Tudors in the sixteenth. Because Ireland lacked an established central monarchy or any political or diplomatic influence, it was perceived as a lacking basic civility and therefore ripe for a more legitimate form of rule...from England. And in fact, England was allowed to do this because there was no European outcry against the conquest. While Scotland had issued the Declaration of Arbroath when threatened by English conquest, calling upon the Pope to legitimize their status as an independent Christian nation, no such political and diplomatic maneuvering was attempted by the Irish against initial rule from England. In effect, Scotland demanded recognition of its status as an equal nation to England and received it, whereas Ireland did not.

Stepping away from the politics, though, we also have to take into account whatever cultural elements were in play before, during, and after the union of these three states. As well-known as the Highlands of Scotland are, and as important a role as they played during the Jacobite Risings, Scottish Gaeldom was only a very small minority of the early modern Scottish state. After the fall of the Lordship of the Isles in 1493, Lowland hegemony over Scotland was well established and Lowland Scots were culturally more similar to the English than they were to either Scottish Highlanders or Irish Gaels. Given that political influence in Scotland was predominantly exercised by Lowlanders, even before the retaliatory legislation enacted following the '45, and that the few Highland magnates (the earl of Argyll comes to mind) who did enjoy a certain amount of power and influence were assiduously 'Lowland' in their cultural outlook (although the Campbells spoke Gaelic and preserved some artistic elements of Gaelic culture around them, their policies were generally very pro-government with the brief exception of the Marian Civil Wars), it is unsurprising that union with Britain went off as easily as it did. Basically, it's important to understand that when it comes to the union of Scotland and England, it wasn't the English coming in and violently forcing the Scots to cooperate, it was the Scottish leaders and politicians who sold their own country out.

Before the Act of Union, the Parliament of Scotland retained full legislative jurisdiction over Scotland and after the Act of Union and the dissolution of the Scottish parliament, a certain number of representative peers and MPs were sent down to Whitehall to advocate for Scottish policy. In Ireland, although an Irish parliament existed, it was confined to voting on taxation alone with all other legislative policy being decided in Whitehall and then enacted by the Lord Lieutenant of Ireland.

And then, of course, we have the issue of religion as has also already been pointed out. Despite the overwhelming majority of the Irish population being Catholic, thanks to the Penal Laws, Catholics were barred from holding political or military office which meant that Ireland was effectively run by the Protestant Anglo-Irish ascendancy who were more or less simply taking orders from Whitehall. The reason that Scots could rise to the rank of general or admiral or government minister was because, with the exception of a few Catholic pockets in the Highlands, the Scottish population were Presbyterian, which, thanks to the language of the Act of Union, exempted them from laws against Catholics and dissenters since the Church of Scotland was granted equality with and independence from the meddling and oversight of the Church of England.

So, it basically boils down to the issue of choice. Scotland was given the option of union and chose it. Ireland was conquered and then strong-armed into actual political union by a government terrified of a joint French-Irish invasion of Britain during the Napoleonic Wars. And, if the recent Scottish Referendum is any indication, Scots even today are still choosing union over independence from England.