I think the NFL is tired of this story and was ready to make it go away especially if it could do so on its terms. Like you said, 100 million is nothing for them as you can see from the numbers presented here.
https://www.cbssports.com/nfl/news/packers-financials-show-that-nfl-made-billions-despite-national-anthem-controversy/Quote
According to financial information released by the Packers on Monday, the NFL distributed more than $8 billion in national revenue that was split among the league's 32 teams. The $8.1 billion in revenue meant that each team received roughly $255 million from the league. According to Bloomberg, the $8.1 billion was a revenue-record for the NFL and a total that was slightly up from the league's revenue total of $7.8 billion in 2016.
100 million spread across 32 teams equates to 3.125 million per team if 2018's numbers are equal to 2017, that's pretty cheap.
I don't believe there was direct collusion by the league or its teams to keep Kaepernick unsigned, I think that was a combination of regressing talent level, salary demands, and outside distractions a team would face by having him on the roster. In short he wasn't worth it This idea might have and probably was communicated by one front office to another. If his talent level was higher then I believe he would have been signed ergo Kareem Hunt, ergo Josh Gordon etc.
All in all while some like you may be disappointed this was the smart move by the league and by Kaepernick. He got the money he wanted and the settlement will serve as evidence to many of his backers that he was correct and the NFL "paid." The NFL doesn't admit it was wrong and the story finally disappears from the headlines and they can go back to making billions of dollars controversy free for now.