The uncompromising Portugal centre-back has also been involved in a number of controversies during his career.
The 29-year-old was accused of stamping on the hand of Barcelona's Lionel Messi last season and earlier this month Real issued a statement defending him over claims he goaded Levante players.
Pepe said: "It is not just against Levante, I think I get a raw deal in about 60% of games.
"If I foul someone, just a regular foul, it is almost like I have half-killed them.
"I feel I get a raw deal from referees but as a professional footballer I have to accept it.
"That is what I do, I roll up my sleeves. I am happy to wear the shirt of Real Madrid."
Pepe was speaking at a press conference at the Etihad Stadium ahead of his side's Champions League Group D match against Manchester City.
Victory would put the Spanish giants in sight of a place in the knockout stages.
Pepe said: "It is a very important game and although we can't finalise qualification, we can make a huge step in the right direction."