On their iron spikes atop the gatehouse, the heads waited. Or so they say, but old ways die hard, as well I know. Supposedly all that had stopped a thousand years ago, when the Boltons had bent their knees to Winterfell. The flayed man was the sigil of House Bolton, Theon knew ages past, certain of their lords had gone so far as to cloak themselves in the skins of dead enemies.
'Lord Bolton, he used to say a naked man has few secrets, but a flayed man's got none.'
'Strip off their skins,' he urged, his thick lips glistening. Reek, actually Ramsay Snow in disguise, suggests flaying people to Theon and actually flays the miller's boys before tarring their heads and putting them on spikes. There's a lot of precedent for the flayed man on as their sigil and there appear to be quite a few specific references of flaying happening in the books and before.