Werner dragged Andreas Lambertz away from a live television interview at the end of his side's 1-1 draw at Borussia Dortmund on Tuesday, claiming that the commentary of the game had been biased against his side.
"It was desolate, denigrating and insulting," he said. "Sooner or later, it reaches a limit we can no longer tolerate.
"I would like more respect for the team. We can live with criticism, but a bit of fairness would be nice."
Werner is not only upset with the treatment his club have received on television.
"Journalists were talking as if it was a minor miracle (that we drew with Dortmund)," he told Kicker magazine.
"Instead, we should be praising the players. (Adam) Bodzek played in a position he's not used to at the centre of the defence, (Leon) Balogun has played one and a half game for us and (Ivan) Paurevic joined us from Borussia's reserve team, and he had only ever seen the stadium before on a tour."
Coach Norbert Meier has also defended his side's style of play, saying: "What do people expect of us?"
"It's obvious that we cannot compete with the quality of Marco Reus.
"I would love to play like Barcelona and have 80% possession in every game, but it doesn't get us anywhere if we play pretty football and concede eight goals.
"Then we would be criticised for getting no points, despite playing prettily."
Points are Meier's priority and the one against the defending Bundesliga champions lifted Fortuna three points away from the relegation zone.
The points have dried up a little for Frankfurt little and they dropped to fifth in the table after losing 3-1 at local rivals Mainz on Tuesday.
"We have got to put that game behind us," said their coach Armin Veh. "Even if we lost, we can learn something from games like that and games like that can bring us closer together."
Veh is without his regular central defenders Carlos Zambrano and Bamba Anderson, but Sebastian Rode will be able to shake off a knock and play.
Fortuna's absence list remains long with Paurevic also missing out due to suspension, but Oliver Fink could return.