Why were Torrhen Stark and his sons so against his daughter marrying Lord Ronnel Arryn?

Torrhen’s sons were not happy with their submission to the Targaryens: “though Torrhen Stark had given up the ancient crown of the Kings of Winter, his sons were less glad of the Targaryen yoke, and some among them entertained talk of rebelling, and of raising the Stark banner whether Lord Torrhen consented or not.” Indeed, much of the North was not happy, hence the formation of the Company of the Rose, “formed by wild men (and, according to some accounts, women) from the North who refused to bend the knee…and instead chose exile across the narrow sea.”

Rhaenys Targaryen was the driving force in making the marriage. While part of her purpose was to “knit together the new, single realm with marriages between the great houses,” another part was to demonstrate that the Iron Throne was the new liege lord of House Stark and had the ultimate authority in dynastic marriages.