The Portuguese coach has come under heavy fire in recent weeks after Barcelona eliminated the capital club from the Champions League, and then went on to win the Spanish title.
Much controversy followed the battles between both clubs, and recent news of Sergio Busquets being let off the hook by Uefa following alleged racist remarks has drawn mixed opinions.
"I'm happy for Sergio Busquets, because he is a Spain team-mate and I wish him well. The only thing that does not seem right or fair is that the only injured party here is Mourinho," Ramos told Marca.com.
"Football has people to take decisions and we cannot do anything," he added, referring to Uefa's actions in relation to the Busquets case.
Ramos was asked whether all the tension whipped up by the Clasicos would affect the national side.
"It would be a grave error if it affected a good and phenomenal group that we have in the team," he said.
"With objectives like the World Cup and European Championships, it should not affect us.
"There was rivalry and tension because there was so much at stake in these games. But you have to forget this and focus on the collective goals that we have."
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