Rooney was given his marching orders after an 80th-minute challenge on City central defender Steve Vickers which left him needing eight stitches in an ankle wound.
Rooney now faces an automatic three-match suspension and Moyes believes it is not even worth appealing against the FA decision because he feels they will close ranks.
Moyes said: "I asked the referee to look at the incident again after the game. Reluctantly he agreed to do that but he wouldn't comment on it.
"There is a decision that could be construed either way. Some people might have said it was a sending off but I think many others would say the opposite.
"If you look at the way Everton have been treated recently I think we'd have to consider that may be the referees are quite keen on us at the moment.
"I think it was a challenge where two players were going for the ball together with the chance of one winning it and the other not winning it.
"I don't think we are getting a fair crack of the whip. I understand the job and I try to help referees but I think at the moment we are not getting the run of things.
"I think Wayne is a victim of that and probably it's also a bit to do with the media saying he is a bit rough and tough.
"It was a good old honest challenge. I did not think it was a red card but there is no point in trying to get it rescinded with the way the FA and referees are at the moment.
"We tried it with David Unsworth and they closed ranks and make sure they get their stories right. I think there is no point in appealing but I think the referee made the wrong decision."
Moyes was unhappy with his side's performance as a goal from US international Jovan Kirovski earned City a share of the spoils after Tomasz Radzinski had put Everton in front.
Moyes said: "I am not happy with a point. We did not play well and it was a poor game in general. Maybe it was a fair result but I am not happy with a point."
Birmingham manager Steve Bruce was left to reflect on more additions to an already crippling injury list which had grown before the game with news that defender Olivier Tebily will be out of action for three to four months with knee ligament damage.
Vickers, Damien Johnson (back) Kirovski (hamstring) and Jeff Horsfield (groin) are now all struggling to play in Saturday's game with Manchester Utd at Old Trafford.
But he praised the fighting qualities of his patched up squad to secure another point which takes them up to the 25 mark for the season and means they have been beaten only once in the last seven games.
Bruce said: "The match was not a spectacle and maybe that is an understatement and our quality and final pass into the area was not good enough.
"But considering the injuries we have piling up it was another worthwhile effort and now we will have to dig deep for the next few games when the injuries and suspensions take effect."
As for the sending off of Rooney, Bruce said: "I am so relieved that I am not talking about one of my players which is what has happened recently all the time.
"All I know is that Vickers is the ultimate professional and he's got eight stitches in his ankle. From where I am watching, it is impossible to judge the tackle so I would not like to make any comment on it."
BIRMINGHAM: Vaesen, Kenna, Vickers, Cunningham, Devlin, Savage, Cisse, Damien Johnson (Lazaridis 43), Michael Johnson, Kirovski (Morrison 61), Horsfield (Hughes 76).
EVERTON: Wright, Weir, Stubbs, Yobo, Pistone, Pembridge (Rooney 66), Naysmith, Gravesen, Carsley, Campbell, Radzinski (Watson 66).
Referee: D Elleray (Middlesex).