That is exactly it. Some people don't understand that. Is he good enough to be in the NFL? Yes I would say he can be a backup on almost all teams.
But why would an owner want a 30 year old backup who will create a media circus everywhere his team goes?
An owner would much rather have a younger, cheaper, potentially better, and non head case as the backup opposed to Kaepernick.
Really isn't that hard to figure out why he is isn't in the league.