Kaepernick had 16 TDs (18 total) to 4 INTs in 11 games in 2016. Most close watchers of quarterbacks agreed Kaepernick played well in 2016. Hoyer went 0-6 with the 49ers last season with far worse stats and he's being touted as a reliable backup in this thread. I'm not sure how to square that circle. Either Hoyer is very bad or Kaepernick is fine, a Tyrod Taylor or Joe Flacco (or Brian Hoyer) tier.
That doesn't mean I don't understand why he's unsigned, as I'm not certain "fine" is worth the headache for teams (whether it should be or not, or whether he deserves the ire he gets, is a different discussion) when they have to actively pursue it, but it's hard to look purely at his stats in 2016 on a very, very bad team and see a guy who would be unemployed the next season.