Complementing System Down's answer, yes the Stark and Bolton rivalry is centuries old when both of them used to be Kings of their own domains.
House Bolton ruled as the Red Kings while the Starks ruled as the Winter Kings. The domain of the Boltons stretched from the Last River to the White Knife and the Sheepshead Hills. Given that both realms were expanding in the aftermath of the Long Night, that soon brought them into direct conflict for dominance over the North.
As System Down suggested, thus began the Bolton tradition of flaying Starks. That was not the full extent of their military successes, Kings Royce II Bolton and Royce IV Bolton even burnt Winterfell after defeating the Starks.
But then the Andal invasion began and the last Red King, Rogar Bolton chose to accept the Starks as their liege Lords instead of fighting the Andals alone and falling like the Southern Kingdoms of the First Men had before. Together, the Starks and the Boltons defeated the Andals and as a result, the North remains the heartland of the First Men and their religion.
As vassals, they have mostly remained loyal to the Starks except a few times when they rebelled. The Boltons and the Greystarks allied against the Starks of Winterfell but lost, House Bolton survived, the Greystarks did not. They also rebelled during reign of King Harlon Stark but bent the knee after a siege of two years.
Roose Bolton's personal motto is "A peaceful land, a quiet people". Neither of those are possible without respecting your Liege Lord's authority. He honored his vows to Winterfell when Eddard Stark called his banners for Robert. He again honored his vows when Robb Stark called the banners.
But as things turned out, the Starks were moving from one disaster to another. Roose figured out that the Starks were bound to lose and he did not plan on being on the losing side. He then got into negotiations with Lord Tywin and the Red Wedding happened.
As for Eddard's relationship, we have no evidence for warm relations or strained relations. Jon however says while Eddard never had a reason to complain of Roose, he never trusted him either.
Eddard Stark had never had any reason to complain of the Lord of the
Dreadfort, so far as Jon knew, but even so he had never trusted him,
with his whispery voice and his pale, pale eyes
ADWD - Jon VII
And also note, Roose doesn't feel like normal people do so let's not assume he hates the Starks. Lady Barbrey Dustin knows him as well as any other person can. She is his former sister-in-law and ally. This is what she says:
Roose has no feelings, you see. Those leeches that he loves so well sucked all the passions out of him years ago. He does not love, he
does not hate, he does not grieve. This is a game to him, mildly
diverting. Some men hunt, some hawk, some tumble dice. Roose plays
with men. You and me, these Freys, Lord Manderly, his plump new wife,
even his bastard, we are but his playthings
ADWD - Prince of Winterfell
It is said over and over again how Roose strikes others as cold and lost to all emotions. So no, Roose probably doesn't hate the Starks. The opportunity was there to rise, he grabbed it and that required him to eliminate the Starks.
Nothing personal, just good business.
So in conclusion:
- Stark-Bolton enmity is not something new.
- Boltons have a royal history which should have encouraged them to be more than vassals to a great House.
- There is no evidence of a Warm relationship between Eddard Stark and Roose Bolton. At the same time, there is no evidence of strained relations either. It was all a professional liege-vassal relationship which was built on duty, self-interests and some suspicion.