Can I ask what makes you think they became "more tolerant" of the Scottish over time? I think I can probably prove that they didn't but I'd like to know what to address directly.

Depending on your timeline it could be argued from various viewpoints- the old favourites: religion, military, economy. Militarily, after political union in 1603, the few Scottish rebellions tended to revolve around dynastic conflict rather than nationalist ambitions (debatable), and after 1745 Scotland aligned its economy with British mercantilism, so both prospered from colonialism and relations improved significantly. Whilst having a large Catholic minority, Scotland tended towards Presbyterianism which conflicted less with England's anti-Catholic agenda.

Ireland on the other hand, was seen from the beginning as a territory to be conquered, and was ruled as a quasi-colony. It had little-to-no central government or leadership, a very primitive agricultural economy, an aggressively nationalistic Catholic majority, who rebelled repeatedly well into the 20th century. Whilst Scotland and England could form a workable partnership, then Ireland was the constant nuisance on the border (from an English perspective). I think the ingrained hatred of Catholicism is the root of this, and possibly a desire to secure borders, as rebellious nobles were exiled and replaced with Scottish Protestants, whilst rebellious peasants were exiled to the west indies as slaves

Follow up question, but with the Welsh. What were their historical attitudes toward the other countries in the British Isles?