Howard is expected to join Colorado Rapids in Major League Soccer this summer, even though he has two years left on his contract.
He was heckled during games against Stoke and Tottenham over Christmas, which led to him gesturing back to fans in the Gwladys Street Stand.
But Martinez said: "I wouldn't say there is a lack of respect from the fans. We all know football is an emotional game. As a fan you watch your team, you want them to perform well and win games. You show your feelings doing that.
"There is a respect towards Tim for what he has done at Everton over the past 10 seasons. Down the line, you'll be looking back on one of Everton's greatest goalkeepers and appreciating that he is an ambassador for the club. He will have that legacy.
"I don't think it is a case of disrespect. It's just the short-term memory and assessment of what you have seen. It's important that Tim doesn't feel all his good work has been forgotten."