Rashford's penalty in United's 5-2 demolition of Bournemouth at Old Trafford was his only goal in his last six matches in all competitions.
"I think everyone is talking about Marcus not scoring a lot of goals but he is doing an amazing job," Fernandes told United's website.
"Maybe he is not achieving his goals and everything but, with everything we are doing now, he will achieve more goals and more assists.
"Football is not just about goals and assists - it is about the team and Marcus is playing very well for the team."
He added: "Marcus was injured for a long time so it's difficult to find that confidence again, to do things like shoot from far out.
"But he is doing an amazing job for the group and I think he deserves credit for this."