If we go by his stats, he was better than almost every current backup QB in the NFL, and also a fair number of starters.
Although the fact remains that after he opted out of his 49ers contract, he turned down a contract offer from Denver, purportedly because he may have ended up being a backup.
As a 49ers fan, my opinion is that he was not handled properly by coach Harbaugh, who tried to turn him into a pocket passer. Kap was the archetype for the current in-demand type of NFL QB (think Lamar Jackson, tho Kap clearly was not that good, as is the case for most QBs not named Patrick Mahomes.)
Clearly his talent (at the time) warranted at least being a backup QB, but he didn't get more than one offer due to his political views.
In other words, his talent was not sufficient to overcome his perceived baggage, since the NFL is (well, was) well known for giving repeat criminal offenders multiple chances, if their talent made the team owners / coaches believe they could help them win.