Atkins had spoken out after Saturday's game when Julian Alsop was shown the red card for a challenge on City keeper Paul Musselwhite.
He said: "The challenge went in, the ref pulled away from it and the Hull players came round and started shoving Alsop, pushing him and got him sent off. You don't like to see that in the game.
"It's certain sections of the media that portray certain people as great coaches, but we can play good football and last season we often played better football than people gave us credit for.
But Tigers boss Taylor has defended the referee's decision to give Alsop his marching orders, and says that Atkins' comments were unfair.
He said: "I've got to say I am very disappointed with Ian Atkins. What he's said about my players is an absolute joke. All they were doing was protecting our goalkeeper.
"For me, Alsop deliberately smashed into the back of Paul Musselwhite. Alsop had already been booked so he had to go. It was the right decision.
"Apparently, Oxford are also saying I criticised their side before the game, which is totally out of order as well.
"If he wants to try and fire-up his own players then that's his choice, but for me, it's very, very poor."