Even though the 28-year-old was benched by former head coach Jim Tomsula halfway into the worst year of his career, Kelly said Kaepernick wants to be a 49er, per Matt Maiocco of CSNBayarea.com:
“He wants to be here,” said Kelly at the NFL Scouting Combine in Indianapolis. “He’s never expressed to me that he doesn’t want to be here. He expressed to me that he was excited about getting healthy and getting going. And we’re excited about him getting healthy and getting going.”
Kaepernick, who signed a six-year, $114 million contract with $61 million guaranteed before the 2015 season, threw just six touchdowns in nine games in 2015 and completed only 59 percent of his passes.
ESPN's Adam Schefter noted 49ers general manager Trent Baalke said the team has no plans to cut Kaepernick before his 2016 guaranteed money kicks in:
49ers GM Trent Baalke said Colin Kaepernick will be on roster April 1, when his $11.9M salary for 2016 becomes guaranteed. Kaep's a Niner.— Adam Schefter (@AdamSchefter) February 24, 2016
However, despite Kelly's and Baalke's assertions, Rand Getlin of NFL Network reported on Thursday night that Kaepernick may indeed be looking to play elsewhere:
Source: Kaepernick's agents have requested permission from the team to seek a trade.— Rand Getlin (@Rand_Getlin) February 25, 2016
If the two sides are not on the same page, it would be hard to blame Kaepernick—who previously expressed interest in playing with the New York Jets, according to NJ Advance Media's Dom Cosentino—for wanting out.
Even though Kelly is not the one who benched Kaepernick, he also has not publicly stated that he will be the starter.
The 49ers also hold the No. 7 pick in the upcoming draft and could take a quarterback—meaning if Kaepernick doesn't show progress, he could find himself on the bench once again.