The 24-year-old is the subject of an online petition calling for him not to be taken to Brazil as part of England's World Cup squad that has amassed more than 15,000 signatures.
However, Martinez, who signed Cleverley on loan while manager of Wigan, is at a loss as to why the England international is being targeted.
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"I don't understand it. Tom is part of this new generation of outstanding English talent," he told reporters.
"There are only a few players who look as if they could have been brought up in Holland or Spain or France because of their understanding of the game, their tactical awareness and their technical quality. Tom has got that.
"Then as a boy, he has got the perfect temperament. He is a level-headed boy.
"I just don't understand this campaign. Tom was maybe given a bigger role than he should have been given but all of a sudden he is being judged like this? He’s young."
Cleverley's national team manager Roy Hodgson defended the midfielder prior to Wednesday's friendly with Denmark, stating he had been singled out as a result of United's difficult campaign.