Why didn’t Stannis’s defeat of the wildlings gain him more popular support in the North?

Well, it did get him popular support – 4,000 soldiers out of 17,000 Northern fighting men remaining joined his side. When you consider that Roose Bolton only had 1,650 men who weren’t Boltons or Freys join his cause, Stannis is winning in a landslide of those who’ve picked a side. 

And he’s likely to win the support of most of the remaining 11,350, as a good chunk of those are Manderly men waiting for Rickon to pledge themselves to his cause.