The Madrid star insists critics only notice when decisions go in his side's favour and never when they go the other way.
Madrid beat Bayern 6-3 on aggregate after Tuesday's quarter-final second leg went to extra time.
The Bundesliga side were furious after two of Cristiano Ronaldo's goals appeared to be offside, while Arturo Vidal was controversially sent off in a match that reignited calls for the adoption of video technology.
But Modric is unhappy with the focus on officiating and feels Madrid would have won the tie regardless.
"I feel sorry that there are controversies after our win against Bayern because I am convinced we were better in two games, created more chances and once again made Manuel Neuer look great," Modric said to Sportske novosti.
"I am used to it now that every refereeing decision in Real's favour gets big publicity and when it goes against us, no one notices it.
"Bayern got a penalty that never was in Munich, Sergio Ramos' own goal came after an offside and Vidal should have got a second yellow in the 47th minute.
"But I don't want to discuss [what Barcelona's Gerard Pique has said about referees].
"I was against VAR in Japan at the Club World Cup because it lasted too long and match officials were not handling it well.
Real's victory means they face city rivals Atletico Madrid in the semi-finals, with Modric relieved to draw Diego Simeone's side now rather than play them again in the final, having won in 2014 and 2016.
The Croatia midfielder said: "It is better to meet Atletico in semi-final than in the final, people would be fed up of the same final three times in last four years.
"Of course it will be very tough, as any match against Atletico is."