I don't think the poll showed a negative perception of the brand Nike at all.
The article says that Nike's favorability dropped from 76% to 60%, and its unfavorability rose from 7% to 24%. I would bet that the change is largely due to the kneejerk reaction of people who have a strong negative opinion of Kaepernick himself.
Read the article again, it specifically points out that they're comparing the new results to the numbers "before the sports apparel giant revealed the former National Football League quarterback as the face of a new marketing campaign."
I think the headline of the article is fair...
"Nike's Colin Kaepernick ad is hurting its brand, poll suggests"
...but even after subtracting the Kaepernick haters, Nike's still at 60% favorable.
And BTW, have you seen the first ad? It's one of the most effective ads I've ever seen, and it's hardly about Colin Kaepernick....
"Trump is what he is, a floundering, inarticulate jumble of gnawing insecurities and not-at-all compensating vanities, which is pathetic."
"How stupid is our country?"