Analysing the Trotters' 2-0 Barclays Premier League defeat to Manchester City on March 3, former Newcastle striker and manager Shearer said Knight had an "absolute shocker", flagging up a number or errors the centre-back had made in the game at the Etihad Stadium.
Coyle dropped Knight for Saturday's 2-1 win over QPR at the Reebok Stadium - which moved Bolton out of the relegation zone - but made it clear he felt Shearer's comments had been in "really poor taste".
The Scot told the BBC: "Like anyone else I sit in on Saturday night and watch Match of the Day and watch us get written off again, but so be it.
"The other disappointing thing is for Alan Shearer to go and pick out one of our individual players - Zat Knight - which I thought was in really poor taste.
"Alan will know, because he had a tough job when he was at Newcastle, how important it is to stick together as a group. The lads are in the studio to give their opinion, but I think it's in poor taste to single out Zat."