The Boltons also had their own vengeance in mind. Remember the Dreadfort has rose up against Winterfell many times in the past to try and become the principal house in the North. The Boltons always bent the knee in the end. Even though it was hundreds of years before, don't think they haven't forgotten. Remember what Tytos Blackwood told Jaime - these old enmities never die. So when the opportunity arises to not only escape destruction, but take vengeance against the Starks and become the ruler of the North, Roose takes it.

This is why I think Robb was really stupid in giving Roose such a huge command. It has been repeated time and time again that his bannermen are not his friends and not to be trusted - at the first sign of weakness they'll turn on you. This is especially true for someone as cold and calculating as Roose. Add the old grudge and you're just asking to be betrayed. Ned always kept a tight grip on Roose because he trusted the Dreadfort least of his bannermen; Robb should have done the same.