Sections of the Real Madrid support aired their displeasure after Bayern led 2-1 at the end of 90 minutes to force extra time in the last-eight affair, although two Ronaldo goals and a Marco Asensio strike in the additional 30 minutes saw the home side comfortably make the semi-finals with an aggregate score of 6-3.
Ronaldo has paid tribute to Bayern for their performance over the two legs, but insists that his team were "fair winners".
"Bayern showed that they were an excellent team, but we played very well," Ronaldo told Antena 3. "We had a lot of chances. We scored two goals. We're used to suffering, but we're very happy.
"Madrid were better, it's not easy to score six goals against Bayern. We're fair winners. I only ask that [the fans] don't whistle me because I always do my best, I work and help Real Madrid. I'll stick with the good things, the team were very good, we played very well."
Ronaldo's hat-trick at the Bernabeu saw him move onto 100 Champions League goals.