The Boltons bid their time, they did nothing to draw Ned Stark's ire.
bide their time? ned 'tolerated' them because they were useful. so honorable but absolutely clueless as to why they run around with a flayed man for a flag and leave fields full of warcrimes everywhere they go
but starks always got time to go tell someone else how to do housecleaning. something about oaths. something about family first.