Martinez, who played a full 90 minutes against Atletico in the 2-0 defeat, went ballistic after the final whistle as he spoke to the media in a fiery interview.
The World Cup winner slammed United, who he said were "really poor" and are a side that "can’t keep changing, changing, changing the manager" due to poor decisions further up at the club.
He went on to say that manager Michael Carrick is not backed enough and that he expects more investment in a side who are out of the EFL Cup and the title race.
Despite his fair criticism, Martinez was torn into by Rooney after his comments went viral, suggesting that the defender is only hurting his teammates by disrespecting them.
"I think Martinez was very premeditated," Rooney said. "Why is he doing the interview after this game? Has he put himself forward, I very rarely hear him speak.
"It looked a bit premeditated and something he spoke about with his team to get out there. It's sad because when you need everyone to stick together as players, you can't be told what's going on above you.
"So you need them players, the manager, the coaching staff to stick together when you're having a difficult time; otherwise, something like that will rip a dressing room apart.
"I think it's a bit disrespectful to his teammates as well because he's disrespecting his teammates; he's saying they're not good enough."
Carrick will now be under further pressure ahead of Sunday’s trip to Leeds where he and his side must pick up three points. Martinez, who has one year left on his United contract, is yet to agree an extension. He may start once more this weekend even after his comments as Carrick seeks a reaction.