Had a quick chat with him 2 years ago during the Niners bye week. I could tell the way he talked about Harbaugh he loved playing for him. Most of the team actually didn't mind his antics since it just showed how much he loved his job and wanted to win. Look up Anthony Davis' twitter feed to also show how he feels about him.
As a Niner fan, the losses this year sucked given the high expectations. But expectations were unreasonable given Bowman was going to be out most of the season (he ended not playing a single game) and Aldon Smith was out for the first 9 games. To add to that, Willis and Williams ended up being out for half the year, Iupati, Davis and Kilgore all missed time (and had to be replaced with Jonathan Martin and a rookie center) which led to a bunch of sacks.
I do blame Harbaugh and the front office for going away from the read option offense to protect their $100M QB investment and appease the primadonnas on the team (Crabtree, Vernon Davis). It's pretty ironic that when the season was done and they opened up the offense for Kaepernick, he ran for over 140 yards. Niners should have ran the same offense Seahawks do.