Ratings were down and polls showed a large minority of fans claimed to be disaffected by Kapernick's protest and those who mimicked it. It was all over the news for about a year.
I also don't think you see how Kaepernick is different from Ray Lewis. Lewis committed a crime, and potentially was involved in a very serious crime. But people weren't personally insulted. A lot of Americans take insults to America personally; the same is true for most nations, because nationalism is a major part of identity for a lot for people. That's why it is such a strong political force. And Kaepernick put himself on the wrong side of that.
Also, if owners don't think Kaep could hurt their bottom line, then why aren't they signing him?