After sending his coded letter to Winterfell, Ned sat down and meditated on his hatred for Ironborn. Wildlings have same culture of raiding and pillaging as Ironborn, so why is Ned hateful of Ironborn but not so of Wildlings. Is it because Wildlings follow same gods as Ned, but Ironborn don't? Is his bais of religious origin? That didn't seem correct answer to Ned.
If not the difference of culture and religion then what? Is it the reasons for said cultures existence, both Wildlings and Ironborn inhabit wastelands unfit for a farming lifestyle, Wildlings due to the cold and Ironborn because of their lands rocky soil. But not all Wildlings raid, do they? They form small communities and settle the land and farm when it is possible or move around in nomadic tribes and subsist on hunting, only few Wildling clans have a culture of raiding and those who raid do so because they are desperate for food, without which they will starve and die. Even girls they stole are considered to be wives and Wildling women have more rights than women in rest of Westeros, they are free to learn to fight and lead as long as they can prove their strength. Only a small percentage of Wildings raid, those that do are desperate for food.
What about Ironborn? Why do they raid and do they need to? Ironborn live on Iron Islands, which are rocky and unfit for farming. But they do have Iron mines, from which their name comes from. Iron Islands are second only to Stromlands in export of Iron. Yes, mining is back breaking work and mining accidents result in horrific casualties, so Ironborn taking up raiding as alternative food source is understandable, but mining techniques have improved over last millennia and Iron Islands are situated in a strategic location and surrounded with bountiful seas, fishing is a readily available food source and the same strategic location that helps them in raiding can also make them excellent traders. Iron Islands could become a trading capital for Western Seven Kingdoms as Kingslanding has become for Eastern Seven Kingdoms, they could grow very rich indeed without ever needing to raid.
So one hand there are some Wildlings clans who raid because they are desperate, there is one option these desperate men could take, they could bend the knee and beg for the Nights Watch to let them past the Wall and beg the Northern Lords to take them in. Even if Wildings forgo their fiercely independent culture and bent the knee will Nights Watch listen, will Northern Lords trust? No, they will be slaughtered before they even speak, such was the centuries deep animosity. On the other hand there are Ironborn, who spurn opportunities they have and disdain paying the ' Gold Price ' as they put it and insist on paying the ' Iron Price ', due to their cultural disdain of the mainland and the people here. And there is the taking of thralls and saltwives, which basically amounts to slavery and rape, which has been abolished in Westeros for millennia and which only few clans of Wildlings practice and those clans are passionately hated by other Wildlings.
After taking all of this into consideration, Ned decided that Ironborn don't need to raid and pillage to survive or even thrive, that is different from Wildlings. Ironborn just do it because it seems easier and because they somehow believe that making their home on a shit stained pile of rocks has made them superior to other men and they have a God given right to prey on other people, maybe because their Drowned God's priests do preach that their God has given them said right.
So, Ned now knew where his hatred for Ironborn comes from, he does hate Wildlings less in part because of their shared ancestry and religion. But most of his hatred for Ironborn comes from their predatory culture.
Identifying root of his hatred is well and good, but Ned needs to work on keeping said hatred in check, after all Ned couldn't be the diplomat for House Stark in the South, when he cannot even keep his emotions in check.